Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP45464
DateThu Jan 5 12:02:41 GMT 2012
Unique Job ID9aa65b035587d68c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d3ckma1
Top template information
Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
Confidence and coverage
Confidence:100.0% Coverage: 46%
311 residues ( 46% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
507 residues ( 75%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MVPSTFSRLKAARCLPVVLAALIFAGCGTHTPDQSTAYMQGTAQADSAFYLQQMQQSSDD
Secondary structure 
SS confidence 
Disorder  ??????????
??????????????????
??????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  TRINWQLLAIRALVKEGKTGQAVELFNQLPQELNDAQRREKTLLAVEIKLAQKDFAGAQN
Secondary structure 
SS confidence 
Disorder 
?????
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  LLAKITPADLEQNQQARYWQAKIDASQGRPSIDLLRALIAQEPLLGAKEKQQNIDATWQA
Secondary structure 
SS confidence 
Disorder 
????????
??
?
????
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LSSMTQEQANTLVINADENILQGWLDLQRVWFDNRNDPDMMKAGIADWQKRYPNNPGAKM
Secondary structure 
SS confidence 
Disorder 
?
?????
?????
?????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LPTQLVNVKAFKPASTNKIALLLPLNGQAAVFGRTIQQGFEAAKNIGTQPVAAQVAAAPA
Secondary structure 
SS confidence 
Disorder  ?
?????
?
????
??????????
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  ADVAEQPQPQTVDGVASPAQASVSDLTGEQPAAQPVPVSAPATSTAAVSAPANPSAELKI
Secondary structure 
SS confidence 
Disorder  ?????????????????????????????????
??????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  YDTSSQPLSQILSQVQQDGASIVVGPLLKNNVEELLKSNTPLNVLALNQPENIENRVNIC
Secondary structure 
SS confidence 
Disorder 
???????
????????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  YFALSPEDEARDAARHIRDQGKQAPLVLIPRSSLGDRVANAFAQEWQKLGGGTVLQQKFG
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  STSELRAGVNGGSGIALTGSPITLRATTDSGMTTNNPTLQTTPTDDQFTNNGGRVDAVYI
Secondary structure 
SS confidence 
Disorder 
???
?????????
????????????????????????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  VATPGEIAFIKPMIAMRNGSQSGATLYASSRSAQGTAGPDFRLEMEGLQYSEIPMLAGGN
Secondary structure 
SS confidence 
Disorder 
????????????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  LPLMQQALSAVNNDYSLARMYAMGVDAWSLANHFSQMRQVQGFEINGNTGSLTANPDCVI
Secondary structure 
SS confidence 
Disorder  ?
????????
????????
Disorder confidence 
 
   .........670........
Sequence  NRNLSWLQYQQGQVVPVS
Secondary structure 
SS confidence 
Disorder 
?
???
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 3ckm chain A domain 1

3D model

Region: 258 - 677
Aligned: 311
Modelled: 314
Confidence: 100.0%
Identity: 38%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 1qo0 chain A

3D model

Region: 255 - 677
Aligned: 327
Modelled: 329
Confidence: 100.0%
Identity: 14%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3hut chain A

3D model

Region: 256 - 677
Aligned: 325
Modelled: 329
Confidence: 100.0%
Identity: 21%
PDB header:transport protein
Chain: A: PDB Molecule:putative branched-chain amino acid abc
PDBTitle: crystal structure of a putative branched-chain amino acid2 abc transporter from rhodospirillum rubrum

Phyre2

PDB 3i09 chain A

3D model

Region: 254 - 672
Aligned: 320
Modelled: 325
Confidence: 100.0%
Identity: 14%
PDB header:transport protein
Chain: A: PDB Molecule:periplasmic branched-chain amino acid-binding protein;
PDBTitle: crystal structure of a periplasmic binding protein (bma2936) from2 burkholderia mallei at 1.80 a resolution

Phyre2

PDB 3t0n chain A

3D model

Region: 253 - 677
Aligned: 329
Modelled: 332
Confidence: 100.0%
Identity: 15%
PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal;
PDBTitle: crystal structure of twin-arginine translocation pathway signal from2 rhodopseudomonas palustris bisb5

Phyre2

PDB 2liv chain A

3D model

Region: 255 - 678
Aligned: 325
Modelled: 330
Confidence: 100.0%
Identity: 15%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3snr chain A

3D model

Region: 254 - 677
Aligned: 322
Modelled: 325
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:extracellular ligand-binding receptor;
PDBTitle: rpd_1889 protein, an extracellular ligand-binding receptor from2 rhodopseudomonas palustris.

Phyre2

PDB 3td9 chain A

3D model

Region: 257 - 678
Aligned: 323
Modelled: 328
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:branched chain amino acid abc transporter, periplasmic
PDBTitle: crystal structure of a leucine binding protein livk (tm1135) from2 thermotoga maritima msb8 at 1.90 a resolution

Phyre2

PDB 3n0w chain A

3D model

Region: 257 - 672
Aligned: 318
Modelled: 323
Confidence: 100.0%
Identity: 15%
PDB header:transport protein
Chain: A: PDB Molecule:abc branched chain amino acid family transporter,
PDBTitle: crystal structure of a branched chain amino acid abc transporter2 periplasmic ligand-binding protein (bxe_c0949) from burkholderia3 xenovorans lb400 at 1.88 a resolution

Phyre2

PDB 3n0x chain A

3D model

Region: 257 - 672
Aligned: 322
Modelled: 326
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:possible substrate binding protein of abc transporter
PDBTitle: crystal structure of an abc-type branched-chain amino acid transporter2 (rpa4397) from rhodopseudomonas palustris cga009 at 1.50 a resolution

Phyre2

PDB 3lkb chain B

3D model

Region: 254 - 678
Aligned: 327
Modelled: 331
Confidence: 100.0%
Identity: 13%
PDB header:transport protein
Chain: B: PDB Molecule:probable branched-chain amino acid abc
PDBTitle: crystal structure of a branched chain amino acid abc2 transporter from thermus thermophilus with bound valine

Phyre2

PDB 1usg chain A

3D model

Region: 255 - 677
Aligned: 324
Modelled: 329
Confidence: 100.0%
Identity: 14%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3h5l chain B

3D model

Region: 250 - 672
Aligned: 327
Modelled: 331
Confidence: 100.0%
Identity: 13%
PDB header:transport protein
Chain: B: PDB Molecule:putative branched-chain amino acid abc
PDBTitle: crystal structure of a putative branched-chain amino acid2 abc transporter from silicibacter pomeroyi

Phyre2

PDB 3i45 chain A

3D model

Region: 255 - 677
Aligned: 327
Modelled: 330
Confidence: 100.0%
Identity: 14%
PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal protein;
PDBTitle: crystal structure of putative twin-arginine translocation pathway2 signal protein from rhodospirillum rubrum atcc 11170

Phyre2

PDB 3ip5 chain A

3D model

Region: 257 - 677
Aligned: 322
Modelled: 327
Confidence: 100.0%
Identity: 13%
PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein (amino acid);
PDBTitle: structure of atu2422-gaba receptor in complex with alanine

Phyre2

PDB 3sg0 chain A

3D model

Region: 254 - 675
Aligned: 320
Modelled: 319
Confidence: 100.0%
Identity: 17%
PDB header:signaling protein
Chain: A: PDB Molecule:extracellular ligand-binding receptor;
PDBTitle: the crystal structure of an extracellular ligand-binding receptor from2 rhodopseudomonas palustris haa2

Phyre2

PDB 3lop chain A

3D model

Region: 257 - 675
Aligned: 323
Modelled: 326
Confidence: 100.0%
Identity: 16%
PDB header:substrate binding protein
Chain: A: PDB Molecule:substrate binding periplasmic protein;
PDBTitle: crystal structure of substrate-binding periplasmic protein2 (pbp) from ralstonia solanacearum

Phyre2

PDB 3eaf chain A

3D model

Region: 257 - 675
Aligned: 322
Modelled: 326
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein;
PDBTitle: crystal structure of abc transporter, substrate binding protein2 aeropyrum pernix

Phyre2

PDB 1jdp chain A

3D model

Region: 253 - 678
Aligned: 329
Modelled: 332
Confidence: 100.0%
Identity: 13%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 1jdp chain A

3D model

Region: 253 - 678
Aligned: 329
Modelled: 332
Confidence: 100.0%
Identity: 13%
PDB header:signaling protein
Chain: A: PDB Molecule:atrial natriuretic peptide clearance receptor;
PDBTitle: crystal structure of hormone/receptor complex

Phyre2

PDB 3ffl chain C

3D model

Region: 48 - 138
Aligned: 91
Modelled: 91
Confidence: 93.2%
Identity: 13%
PDB header:cell cycle
Chain: C: PDB Molecule:anaphase-promoting complex subunit 7;
PDBTitle: crystal structure of the n-terminal domain of anaphase-2 promoting complex subunit 7

Phyre2

PDB 2xcb chain A

3D model

Region: 59 - 187
Aligned: 126
Modelled: 126
Confidence: 93.1%
Identity: 10%
PDB header:protein binding
Chain: A: PDB Molecule:regulatory protein pcrh;
PDBTitle: crystal structure of pcrh in complex with the chaperone2 binding region of popd

Phyre2

PDB 2kc7 chain A

3D model

Region: 66 - 155
Aligned: 89
Modelled: 89
Confidence: 92.7%
Identity: 19%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:bfr218_protein;
PDBTitle: solution nmr structure of bacteroides fragilis protein2 bf1650. northeast structural genomics consortium target3 bfr218

Phyre2

PDB 3k9i chain A

3D model

Region: 45 - 150
Aligned: 104
Modelled: 103
Confidence: 91.5%
Identity: 13%
PDB header:protein binding
Chain: A: PDB Molecule:bh0479 protein;
PDBTitle: crystal structure of putative protein binding protein (np_241345.1)2 from bacillus halodurans at 2.71 a resolution

Phyre2

PDB 3hym chain B

3D model

Region: 61 - 250
Aligned: 188
Modelled: 181
Confidence: 91.1%
Identity: 5%
PDB header:cell cycle, ligase
Chain: B: PDB Molecule:cell division cycle protein 16 homolog;
PDBTitle: insights into anaphase promoting complex tpr subdomain2 assembly from a cdc26-apc6 structure

Phyre2

PDB 2r5s chain B

3D model

Region: 66 - 231
Aligned: 159
Modelled: 158
Confidence: 91.0%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein vp0806;
PDBTitle: the crystal structure of a domain of protein vp0806 (unknown function)2 from vibrio parahaemolyticus rimd 2210633

Phyre2

PDB 3pe3 chain D

3D model

Region: 58 - 242
Aligned: 181
Modelled: 181
Confidence: 89.3%
Identity: 10%
PDB header:transferase
Chain: D: PDB Molecule:udp-n-acetylglucosamine--peptide n-
PDBTitle: structure of human o-glcnac transferase and its complex with a peptide2 substrate

Phyre2
1
d3ckma1
2
d1qo0a_
3
c3hutA_
4
c3i09A_
5
c3t0nA_
6
d2liva_
7
c3snrA_
8
c3td9A_
9
c3n0wA_
10
c3n0xA_
11
c3lkbB_
12
d1usga_
13
c3h5lB_
14
c3i45A_
15
c3ip5A_
16
c3sg0A_
17
c3lopA_
18
c3eafA_
19
d1jdpa_
20
c1jdpA_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
c3fflC_
101
c2xcbA_
102
c2kc7A_
103
104
105
106
107
c3k9iA_
108
c3hymB_
109
c2r5sB_
110
111
c3pe3D_
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d3ckma1
100.0 38 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
2d1qo0a_
100.0 14 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
3c3hutA_
100.0 21 PDB header:transport protein
Chain: A: PDB Molecule:putative branched-chain amino acid abc
PDBTitle: crystal structure of a putative branched-chain amino acid2 abc transporter from rhodospirillum rubrum
4c3i09A_
100.0 14 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic branched-chain amino acid-binding protein;
PDBTitle: crystal structure of a periplasmic binding protein (bma2936) from2 burkholderia mallei at 1.80 a resolution
5c3t0nA_
100.0 15 PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal;
PDBTitle: crystal structure of twin-arginine translocation pathway signal from2 rhodopseudomonas palustris bisb5
6d2liva_
100.0 15 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
7c3snrA_
100.0 18 PDB header:transport protein
Chain: A: PDB Molecule:extracellular ligand-binding receptor;
PDBTitle: rpd_1889 protein, an extracellular ligand-binding receptor from2 rhodopseudomonas palustris.
8c3td9A_
100.0 18 PDB header:transport protein
Chain: A: PDB Molecule:branched chain amino acid abc transporter, periplasmic
PDBTitle: crystal structure of a leucine binding protein livk (tm1135) from2 thermotoga maritima msb8 at 1.90 a resolution
9c3n0wA_
100.0 15 PDB header:transport protein
Chain: A: PDB Molecule:abc branched chain amino acid family transporter,
PDBTitle: crystal structure of a branched chain amino acid abc transporter2 periplasmic ligand-binding protein (bxe_c0949) from burkholderia3 xenovorans lb400 at 1.88 a resolution
10c3n0xA_
100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:possible substrate binding protein of abc transporter
PDBTitle: crystal structure of an abc-type branched-chain amino acid transporter2 (rpa4397) from rhodopseudomonas palustris cga009 at 1.50 a resolution
11c3lkbB_
100.0 13 PDB header:transport protein
Chain: B: PDB Molecule:probable branched-chain amino acid abc
PDBTitle: crystal structure of a branched chain amino acid abc2 transporter from thermus thermophilus with bound valine
12d1usga_
100.0 14 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
13c3h5lB_
100.0 13 PDB header:transport protein
Chain: B: PDB Molecule:putative branched-chain amino acid abc
PDBTitle: crystal structure of a putative branched-chain amino acid2 abc transporter from silicibacter pomeroyi
14c3i45A_
100.0 14 PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal protein;
PDBTitle: crystal structure of putative twin-arginine translocation pathway2 signal protein from rhodospirillum rubrum atcc 11170
15c3ip5A_
100.0 13 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein (amino acid);
PDBTitle: structure of atu2422-gaba receptor in complex with alanine
16c3sg0A_
100.0 17 PDB header:signaling protein
Chain: A: PDB Molecule:extracellular ligand-binding receptor;
PDBTitle: the crystal structure of an extracellular ligand-binding receptor from2 rhodopseudomonas palustris haa2
17c3lopA_
100.0 16 PDB header:substrate binding protein
Chain: A: PDB Molecule:substrate binding periplasmic protein;
PDBTitle: crystal structure of substrate-binding periplasmic protein2 (pbp) from ralstonia solanacearum
18c3eafA_
100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein;
PDBTitle: crystal structure of abc transporter, substrate binding protein2 aeropyrum pernix
19d1jdpa_
100.0 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
20c1jdpA_
100.0 13 PDB header:signaling protein
Chain: A: PDB Molecule:atrial natriuretic peptide clearance receptor;
PDBTitle: crystal structure of hormone/receptor complex
21c1yk1B_
not modelled 100.0 11 PDB header:hormone/growth factor receptor
Chain: B: PDB Molecule:atrial natriuretic peptide clearance receptor;
PDBTitle: structure of natriuretic peptide receptor-c complexed with brain2 natriuretic peptide
22c3om1A_
not modelled 100.0 12 PDB header:membrane protein
Chain: A: PDB Molecule:glutamate receptor gluk5 (ka2);
PDBTitle: crystal structure of the gluk5 (ka2) atd dimer at 1.7 angstrom2 resolution
23d1dp4a_
not modelled 100.0 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
24c3h6hB_
not modelled 100.0 10 PDB header:membrane protein
Chain: B: PDB Molecule:glutamate receptor, ionotropic kainate 2;
PDBTitle: crystal structure of the glur6 amino terminal domain dimer assembly2 mpd form
25c3sm9A_
not modelled 100.0 16 PDB header:signaling protein
Chain: A: PDB Molecule:metabotropic glutamate receptor 3;
PDBTitle: crystal structure of metabotropic glutamate receptor 3 precursor in2 presence of ly341495 antagonist
26d1ewka_
not modelled 100.0 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
27c2e4zA_
not modelled 100.0 15 PDB header:signaling protein
Chain: A: PDB Molecule:metabotropic glutamate receptor 7;
PDBTitle: crystal structure of the ligand-binding region of the group iii2 metabotropic glutamate receptor
28c3sajB_
not modelled 100.0 14 PDB header:transport protein
Chain: B: PDB Molecule:glutamate receptor 1;
PDBTitle: crystal structure of glutamate receptor glua1 amino terminal domain
29c3kg2A_
not modelled 100.0 16 PDB header:membrane protein, transport protein
Chain: A: PDB Molecule:glutamate receptor 2;
PDBTitle: ampa subtype ionotropic glutamate receptor in complex with competitive2 antagonist zk 200775
30c3p3wC_
not modelled 100.0 12 PDB header:transport protein
Chain: C: PDB Molecule:glutamate receptor 3;
PDBTitle: structure of a dimeric glua3 n-terminal domain (ntd) at 4.2 a2 resolution
31c2e4wA_
not modelled 100.0 17 PDB header:signaling protein
Chain: A: PDB Molecule:metabotropic glutamate receptor 3;
PDBTitle: crystal structure of the extracellular region of the group ii2 metabotropic glutamate receptor complexed with 1s,3s-acpd
32c2wjxA_
not modelled 99.9 13 PDB header:transport protein
Chain: A: PDB Molecule:glutamate receptor 2;
PDBTitle: crystal structure of the human ionotropic glutamate2 receptor glur2 atd region at 4.1 a resolution
33c3q41B_
not modelled 99.9 18 PDB header:transport protein
Chain: B: PDB Molecule:glutamate [nmda] receptor subunit zeta-1;
PDBTitle: crystal structure of the glun1 n-terminal domain (ntd)
34c3jpyA_
not modelled 99.7 14 PDB header:transport protein
Chain: A: PDB Molecule:glutamate [nmda] receptor subunit epsilon-2;
PDBTitle: crystal structure of the zinc-bound amino terminal domain of the nmda2 receptor subunit nr2b
35c2iksA_
not modelled 98.6 16 PDB header:transcription
Chain: A: PDB Molecule:dna-binding transcriptional dual regulator;
PDBTitle: crystal structure of n-terminal truncated dna-binding transcriptional2 dual regulator from escherichia coli k12
36c3h5oB_
not modelled 98.5 15 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator gntr;
PDBTitle: the crystal structure of transcription regulator gntr from2 chromobacterium violaceum
37c3mizB_
not modelled 98.5 14 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator protein, laci
PDBTitle: crystal structure of a putative transcriptional regulator2 protein, lacl family from rhizobium etli
38c3g85A_
not modelled 98.4 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (laci family);
PDBTitle: crystal structure of laci family transcription regulator from2 clostridium acetobutylicum
39c3d8uA_
not modelled 98.4 15 PDB header:transcription regulator
Chain: A: PDB Molecule:purr transcriptional regulator;
PDBTitle: the crystal structure of a purr family transcriptional regulator from2 vibrio parahaemolyticus rimd 2210633
40c3c3kA_
not modelled 98.4 9 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of an uncharacterized protein from actinobacillus2 succinogenes
41c3brqA_
not modelled 98.4 10 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator ascg;
PDBTitle: crystal structure of the escherichia coli transcriptional repressor2 ascg
42c3dbiA_
not modelled 98.3 11 PDB header:transcription regulator
Chain: A: PDB Molecule:sugar-binding transcriptional regulator, laci family;
PDBTitle: crystal structure of sugar-binding transcriptional regulator (laci2 family) from escherichia coli complexed with phosphate
43c2rjoA_
not modelled 98.3 17 PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal protein;
PDBTitle: crystal structure of twin-arginine translocation pathway signal2 protein from burkholderia phytofirmans
44c3gv0A_
not modelled 98.3 19 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of laci family transcription regulator from2 agrobacterium tumefaciens
45c3e3mA_
not modelled 98.3 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a laci family transcriptional2 regulator from silicibacter pomeroyi
46c3k4hA_
not modelled 98.3 10 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator laci from2 bacillus cereus subsp. cytotoxis nvh 391-98
47c3k9cA_
not modelled 98.3 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family protein;
PDBTitle: crystal structure of laci transcriptional regulator from rhodococcus2 species.
48c3qk7C_
not modelled 98.3 15 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulators;
PDBTitle: crystal structure of putative transcriptional regulator from yersinia2 pestis biovar microtus str. 91001
49d1jx6a_
not modelled 98.3 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
50c3hcwB_
not modelled 98.3 9 PDB header:rna binding protein
Chain: B: PDB Molecule:maltose operon transcriptional repressor;
PDBTitle: crystal structure of probable maltose operon transcriptional repressor2 malr from staphylococcus areus
51c2rgyA_
not modelled 98.3 12 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of transcriptional regulator of laci family from2 burkhoderia phymatum
52d1tjya_
not modelled 98.1 14 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
53c3ksmA_
not modelled 98.1 14 PDB header:transport protein
Chain: A: PDB Molecule:abc-type sugar transport system, periplasmic component;
PDBTitle: crystal structure of abc-type sugar transport system, periplasmic2 component from hahella chejuensis
54c3o1hB_
not modelled 98.0 16 PDB header:signaling protein
Chain: B: PDB Molecule:periplasmic protein tort;
PDBTitle: crystal structure of the tors sensor domain - tort complex in the2 presence of tmao
55d2nzug1
not modelled 98.0 10 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
56c2qu7B_
not modelled 98.0 10 PDB header:transcription
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of a putative transcription regulator2 from staphylococcus saprophyticus subsp. saprophyticus
57c3bblA_
not modelled 97.9 9 PDB header:regulatory protein
Chain: A: PDB Molecule:regulatory protein of laci family;
PDBTitle: crystal structure of a regulatory protein of laci family from2 chloroflexus aggregans
58c3cs3A_
not modelled 97.9 16 PDB header:transcription regulator
Chain: A: PDB Molecule:sugar-binding transcriptional regulator, laci family;
PDBTitle: crystal structure of sugar-binding transcriptional regulator (laci2 family) from enterococcus faecalis
59c3egcF_
not modelled 97.9 15 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative ribose operon repressor;
PDBTitle: crystal structure of a putative ribose operon repressor from2 burkholderia thailandensis
60d1gcaa_
not modelled 97.8 16 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
61c3h75A_
not modelled 97.8 10 PDB header:sugar binding protein
Chain: A: PDB Molecule:periplasmic sugar-binding domain protein;
PDBTitle: crystal structure of a periplasmic sugar-binding protein from the2 pseudomonas fluorescens
62c2fqxA_
not modelled 97.6 17 PDB header:transport protein
Chain: A: PDB Molecule:membrane lipoprotein tmpc;
PDBTitle: pnra from treponema pallidum complexed with guanosine
63c2ioyB_
not modelled 97.6 17 PDB header:sugar binding protein
Chain: B: PDB Molecule:periplasmic sugar-binding protein;
PDBTitle: crystal structure of thermoanaerobacter tengcongensis2 ribose binding protein
64c3lftA_
not modelled 97.6 15 PDB header:structure genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: the crystal structure of the abc domain in complex with l-trp from2 streptococcus pneumonia to 1.35a
65c3jy6B_
not modelled 97.6 19 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of laci transcriptional regulator from lactobacillus2 brevis
66c2h0aA_
not modelled 97.6 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of probable transcription regulator from2 thermus thermophilus
67d1jyea_
not modelled 97.5 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
68c1jyeA_
not modelled 97.5 12 PDB header:transcription
Chain: A: PDB Molecule:lactose operon repressor;
PDBTitle: structure of a dimeric lac repressor with c-terminal deletion and k84l2 substitution
69c2o20H_
not modelled 97.5 9 PDB header:transcription
Chain: H: PDB Molecule:catabolite control protein a;
PDBTitle: crystal structure of transcription regulator ccpa of lactococcus2 lactis
70c3ma0A_
not modelled 97.5 18 PDB header:sugar binding protein
Chain: A: PDB Molecule:d-xylose-binding periplasmic protein;
PDBTitle: closed liganded crystal structure of xylose binding protein from2 escherichia coli
71d1guda_
not modelled 97.5 15 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
72c2vk2A_
not modelled 97.5 14 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter periplasmic-binding protein ytfq;
PDBTitle: crystal structure of a galactofuranose binding protein
73c3gybB_
not modelled 97.5 14 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulators (laci-family
PDBTitle: crystal structure of a laci-family transcriptional2 regulatory protein from corynebacterium glutamicum
74c3brsA_
not modelled 97.4 13 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic binding protein/laci transcriptional regulator;
PDBTitle: crystal structure of sugar transporter from clostridium2 phytofermentans
75c3kkeA_
not modelled 97.4 15 PDB header:transcription regulator
Chain: A: PDB Molecule:laci family transcriptional regulator;
PDBTitle: crystal structure of a laci family transcriptional regulator2 from mycobacterium smegmatis
76c3jvdA_
not modelled 97.3 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulators;
PDBTitle: crystal structure of putative transcription regulation repressor (laci2 family) from corynebacterium glutamicum
77c2fn9A_
not modelled 97.3 11 PDB header:sugar binding protein
Chain: A: PDB Molecule:ribose abc transporter, periplasmic ribose-binding protein;
PDBTitle: thermotoga maritima ribose binding protein unliganded form
78c3clkB_
not modelled 97.2 6 PDB header:transcription regulator
Chain: B: PDB Molecule:transcription regulator;
PDBTitle: crystal structure of a transcription regulator from lactobacillus2 plantarum
79d2dria_
not modelled 97.2 16 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
80c3d02A_
not modelled 97.2 13 PDB header:sugar binding protein
Chain: A: PDB Molecule:putative laci-type transcriptional regulator;
PDBTitle: crystal structure of periplasmic sugar-binding protein2 (yp_001338366.1) from klebsiella pneumoniae subsp. pneumoniae mgh3 78578 at 1.30 a resolution
81c2qvcC_
not modelled 97.1 13 PDB header:transport protein
Chain: C: PDB Molecule:sugar abc transporter, periplasmic sugar-binding
PDBTitle: crystal structure of a periplasmic sugar abc transporter2 from thermotoga maritima
82c1zvvA_
not modelled 97.1 12 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
83c3ctpB_
not modelled 97.0 12 PDB header:transcription regulator
Chain: B: PDB Molecule:periplasmic binding protein/laci transcriptional regulator;
PDBTitle: crystal structure of periplasmic binding protein/laci transcriptional2 regulator from alkaliphilus metalliredigens qymf complexed with d-3 xylulofuranose
84d8abpa_
not modelled 97.0 8 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
85c2hqbA_
not modelled 96.8 10 PDB header:transcription
Chain: A: PDB Molecule:transcriptional activator of comk gene;
PDBTitle: crystal structure of a transcriptional activator of comk2 gene from bacillus halodurans
86c2dgdD_
not modelled 96.7 13 PDB header:lyase
Chain: D: PDB Molecule:223aa long hypothetical arylmalonate decarboxylase;
PDBTitle: crystal structure of st0656, a function unknown protein from2 sulfolobus tokodaii
87c2xecD_
not modelled 96.7 13 PDB header:isomerase
Chain: D: PDB Molecule:putative maleate isomerase;
PDBTitle: nocardia farcinica maleate cis-trans isomerase bound to2 tris
88c2qh8A_
not modelled 96.7 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of conserved domain protein from vibrio2 cholerae o1 biovar eltor str. n16961
89d1byka_
not modelled 96.7 15 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
90c3bilA_
not modelled 96.6 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:probable laci-family transcriptional regulator;
PDBTitle: crystal structure of a probable laci family transcriptional2 regulator from corynebacterium glutamicum
91c3g1wB_
not modelled 96.5 7 PDB header:transport protein
Chain: B: PDB Molecule:sugar abc transporter;
PDBTitle: crystal structure of sugar abc transporter (sugar-binding protein)2 from bacillus halodurans
92c2x7xA_
not modelled 96.5 8 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: fructose binding periplasmic domain of hybrid two component2 system bt1754
93d2fvya1
not modelled 96.0 17 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
94c3l6uA_
not modelled 95.9 10 PDB header:transport protein
Chain: A: PDB Molecule:abc-type sugar transport system periplasmic
PDBTitle: crystal structure of abc-type sugar transport system,2 periplasmic component from exiguobacterium sibiricum
95c3s99A_
not modelled 95.5 8 PDB header:lipid binding protein
Chain: A: PDB Molecule:basic membrane lipoprotein;
PDBTitle: crystal structure of a basic membrane lipoprotein from brucella2 melitensis, iodide soak
96c2vlbC_
not modelled 95.4 14 PDB header:lyase
Chain: C: PDB Molecule:arylmalonate decarboxylase;
PDBTitle: structure of unliganded arylmalonate decarboxylase
97d1dbqa_
not modelled 95.3 14 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
98c3o74A_
not modelled 95.3 16 PDB header:transcription
Chain: A: PDB Molecule:fructose transport system repressor frur;
PDBTitle: crystal structure of cra transcriptional dual regulator from2 pseudomonas putida
99c3e61A_
not modelled 94.3 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative transcriptional repressor of ribose operon;
PDBTitle: crystal structure of a putative transcriptional repressor of ribose2 operon from staphylococcus saprophyticus subsp. saprophyticus
100c3fflC_
93.2 13 PDB header:cell cycle
Chain: C: PDB Molecule:anaphase-promoting complex subunit 7;
PDBTitle: crystal structure of the n-terminal domain of anaphase-2 promoting complex subunit 7
101c2xcbA_
93.1 10 PDB header:protein binding
Chain: A: PDB Molecule:regulatory protein pcrh;
PDBTitle: crystal structure of pcrh in complex with the chaperone2 binding region of popd
102c2kc7A_
92.7 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:bfr218_protein;
PDBTitle: solution nmr structure of bacteroides fragilis protein2 bf1650. northeast structural genomics consortium target3 bfr218
103d1tlfa_
not modelled 92.5 14 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
104c3rotA_
not modelled 92.4 11 PDB header:transport protein
Chain: A: PDB Molecule:abc sugar transporter, periplasmic sugar binding protein;
PDBTitle: crystal structure of abc sugar transporter (periplasmic sugar binding2 protein) from legionella pneumophila
105c3kjxD_
not modelled 92.3 15 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
106c3hs3A_
not modelled 91.7 11 PDB header:transcription regulator
Chain: A: PDB Molecule:ribose operon repressor;
PDBTitle: crystal structure of periplasmic binding ribose operon2 repressor protein from lactobacillus acidophilus
107c3k9iA_
91.5 13 PDB header:protein binding
Chain: A: PDB Molecule:bh0479 protein;
PDBTitle: crystal structure of putative protein binding protein (np_241345.1)2 from bacillus halodurans at 2.71 a resolution
108c3hymB_
91.1 5 PDB header:cell cycle, ligase
Chain: B: PDB Molecule:cell division cycle protein 16 homolog;
PDBTitle: insights into anaphase promoting complex tpr subdomain2 assembly from a cdc26-apc6 structure
109c2r5sB_
91.0 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein vp0806;
PDBTitle: the crystal structure of a domain of protein vp0806 (unknown function)2 from vibrio parahaemolyticus rimd 2210633
110c2xevB_
not modelled 90.4 12 PDB header:metal binding
Chain: B: PDB Molecule:ybgf;
PDBTitle: crystal structure of the tpr domain of xanthomonas2 campestris ybgf
111c3pe3D_
89.3 10 PDB header:transferase
Chain: D: PDB Molecule:udp-n-acetylglucosamine--peptide n-
PDBTitle: structure of human o-glcnac transferase and its complex with a peptide2 substrate
112c3l49D_
not modelled 88.2 8 PDB header:transport protein
Chain: D: PDB Molecule:abc sugar (ribose) transporter, periplasmic
PDBTitle: crystal structure of abc sugar transporter subunit from2 rhodobacter sphaeroides 2.4.1
113c3gbvB_
not modelled 88.2 17 PDB header:transcription regulator
Chain: B: PDB Molecule:putative laci-family transcriptional regulator;
PDBTitle: crystal structure of a putative laci transcriptional regulator from2 bacteroides fragilis
114c3huuC_
not modelled 87.9 11 PDB header:transcription regulator
Chain: C: PDB Molecule:transcription regulator like protein;
PDBTitle: crystal structure of transcription regulator like protein from2 staphylococcus haemolyticus
115c2xpiA_
not modelled 87.8 12 PDB header:cell cycle
Chain: A: PDB Molecule:anaphase-promoting complex subunit cut9;
PDBTitle: crystal structure of apc/c hetero-tetramer cut9-hcn1
116c2dbaA_
not modelled 86.7 13 PDB header:structural protein
Chain: A: PDB Molecule:smooth muscle cell associated protein-1, isoform
PDBTitle: the solution structure of the tetratrico peptide repeat of2 human smooth muscle cell associated protein-1, isoform 2
117c3urzB_
not modelled 85.5 11 PDB header:protein binding
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a hypothetical protein (bacova_03105) from2 bacteroides ovatus atcc 8483 at 2.19 a resolution
118d1zbpa1
not modelled 85.2 19 Fold:ImpE-like
Superfamily:ImpE-like
Family:ImpE-like
119d1w3ba_
not modelled 85.2 12 Fold:alpha-alpha superhelix
Superfamily:TPR-like
Family:Tetratricopeptide repeat (TPR)
120c3mv3B_
not modelled 84.7 11 PDB header:protein transport
Chain: B: PDB Molecule:coatomer subunit epsilon;
PDBTitle: crystal structure of a-cop in complex with e-cop

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite


Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0