Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77698
DateThu Jan 5 12:31:47 GMT 2012
Unique Job IDe615bbdb963a1a78

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2r0qF_
Top template information
PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
Confidence and coverage
Confidence: 99.9% Coverage: 37%
188 residues ( 37% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKKAIAYMRFSSPGQMSGDSLNRQRRLIAEWLKVNSDYYLDTITYEDLGLSAFKGKHAQS
Secondary structure 
SS confidence 
Disorder  ?
??????
????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GAFSEFLDAIEHGYILPGTTLLVESLDRLSREKVGEAIERLKLILNHGIDVITLCDNTVY
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  NIDSLNEPYSLIKAILIAQRANEESEIKSSRVKLSWKKKRQDALESGTIMTASCPRWLSL
Secondary structure 
SS confidence 
Disorder 
??
??
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  DDKRTAFVPDPDRVKTIELIFKLRMERRSLNAIAKYLNDHAVKNFSGKESAWGPSVIEKL
Secondary structure 
SS confidence 
Disorder 
?
???
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LANKALIGICVPSYRARGKGISEIAGYYPRVISDDLFYAVQEIRLAPFGISNSSKNPMLI
Secondary structure 
SS confidence 
Disorder 
??????
?????????????
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  NLLRTVMKCEACGNTMIVHAVSGSLHGYYVCPMRRLHRCDRPSIKRDLVDYNIINELLFN
Secondary structure 
SS confidence 
Disorder 
???
???????
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  CSKIQPVENKKDANETLELKIIELQMKINNLIVALSVAPEVTAIAEKIRLLDKELRRASV
Secondary structure 
SS confidence 
Disorder 
?
??
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  SLKTLKSKGVNSFSDFYAIDLTSKNGRELCRTLAYKTFEKIIINTDNKTCDIYFMNGIVF
Secondary structure 
SS confidence 
Disorder 
??
??
Disorder confidence 
 
   .........490.........500........
Sequence  KHYPLMKVISAQQAISALKYMVDGEIYF
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 2r0q chain F

3D model

Region: 1 - 243
Aligned: 188
Modelled: 210
Confidence: 99.9%
Identity: 20%
PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex

Phyre2

PDB 3guv chain A

3D model

Region: 3 - 162
Aligned: 147
Modelled: 160
Confidence: 99.9%
Identity: 22%
PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein;
PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae

Phyre2

PDB 2gm4 chain B

3D model

Region: 4 - 242
Aligned: 174
Modelled: 216
Confidence: 99.9%
Identity: 21%
PDB header:recombination, dna
Chain: B: PDB Molecule:transposon gamma-delta resolvase;
PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna

Phyre2

PDB 3g13 chain B

3D model

Region: 1 - 147
Aligned: 135
Modelled: 145
Confidence: 99.9%
Identity: 16%
PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile

Phyre2

PDB 1gdt chain A domain 2

3D model

Region: 1 - 164
Aligned: 138
Modelled: 163
Confidence: 99.8%
Identity: 20%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3bvp chain B

3D model

Region: 2 - 148
Aligned: 129
Modelled: 147
Confidence: 99.8%
Identity: 27%
PDB header:recombination
Chain: B: PDB Molecule:tp901-1 integrase;
PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase

Phyre2

PDB 3lhk chain A

3D model

Region: 2 - 162
Aligned: 139
Modelled: 156
Confidence: 99.8%
Identity: 19%
PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna binding protein mj0014;
PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii.

Phyre2

PDB 2gm4 chain A domain 2

3D model

Region: 1 - 164
Aligned: 134
Modelled: 164
Confidence: 99.8%
Identity: 20%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3lhf chain C

3D model

Region: 2 - 161
Aligned: 133
Modelled: 160
Confidence: 99.8%
Identity: 23%
PDB header:recombination
Chain: C: PDB Molecule:serine recombinase;
PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a

Phyre2

PDB 3pkz chain K

3D model

Region: 1 - 144
Aligned: 121
Modelled: 141
Confidence: 99.7%
Identity: 23%
PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase

Phyre2

PDB 2rsl chain A

3D model

Region: 1 - 148
Aligned: 115
Modelled: 131
Confidence: 99.7%
Identity: 24%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 3plo chain X

3D model

Region: 4 - 152
Aligned: 122
Modelled: 140
Confidence: 99.7%
Identity: 25%
PDB header:recombination
Chain: X: PDB Molecule:dna-invertase;
PDBTitle: crystal structure of the fis-independent mutant of gin

Phyre2

PDB 1hx7 chain A

3D model

Region: 1 - 125
Aligned: 104
Modelled: 115
Confidence: 99.5%
Identity: 23%
Fold: Resolvase-like
Superfamily: Resolvase-like
Family: gamma,delta resolvase, catalytic domain

Phyre2

PDB 1u78 chain A

3D model

Region: 198 - 288
Aligned: 65
Modelled: 78
Confidence: 88.4%
Identity: 17%
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna

Phyre2

PDB 3cng chain C

3D model

Region: 308 - 335
Aligned: 28
Modelled: 28
Confidence: 86.5%
Identity: 29%
PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea

Phyre2

PDB 1i3q chain I

3D model

Region: 303 - 336
Aligned: 34
Modelled: 34
Confidence: 83.8%
Identity: 15%
PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd
PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution

Phyre2

PDB 3ghg chain K

3D model

Region: 365 - 452
Aligned: 88
Modelled: 88
Confidence: 80.4%
Identity: 8%
PDB header:blood clotting
Chain: K: PDB Molecule:fibrinogen beta chain;
PDBTitle: crystal structure of human fibrinogen

Phyre2

PDB 1deq chain F

3D model

Region: 365 - 460
Aligned: 96
Modelled: 96
Confidence: 76.5%
Identity: 10%
PDB header:
PDB COMPND:

Phyre2

PDB 2gb5 chain B

3D model

Region: 308 - 336
Aligned: 25
Modelled: 29
Confidence: 73.3%
Identity: 20%
PDB header:hydrolase
Chain: B: PDB Molecule:nadh pyrophosphatase;
PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution

Phyre2

PDB 2opf chain A

3D model

Region: 274 - 334
Aligned: 58
Modelled: 61
Confidence: 72.2%
Identity: 22%
PDB header:hydrolase/dna
Chain: A: PDB Molecule:endonuclease viii;
PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate

Phyre2

PDB 1dgs chain A domain 1

3D model

Region: 308 - 346
Aligned: 30
Modelled: 30
Confidence: 59.1%
Identity: 20%
Fold: SAM domain-like
Superfamily: RuvA domain 2-like
Family: NAD+-dependent DNA ligase, domain 3

Phyre2

PDB 2dq3 chain A

3D model

Region: 345 - 434
Aligned: 90
Modelled: 90
Confidence: 57.8%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: crystal structure of aq_298

Phyre2
1
c2r0qF_
2
c3guvA_
3
c2gm4B_
4
c3g13B_
5
d1gdta2
6
c3bvpB_
7
c3lhkA_
8
d2gm4a2
9
c3lhfC_
10
c3pkzK_
11
d2rsla_
12
c3ploX_
13
d1hx7a_
14
c1u78A_
15
c3cngC_
16
c1i3qI_
17
c3ghgK_
18
c1deqF_
19
c2gb5B_
20
c2opfA_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
d1dgsa1
36
37
c2dq3A_
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
101
102
103
104
105
106
107
108
109
110
111
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2r0qF_
99.9 20 PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
2c3guvA_
99.9 22 PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein;
PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae
3c2gm4B_
99.9 21 PDB header:recombination, dna
Chain: B: PDB Molecule:transposon gamma-delta resolvase;
PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
4c3g13B_
99.9 16 PDB header:recombination
Chain: B: PDB Molecule:putative conjugative transposon recombinase;
PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile
5d1gdta2
99.8 20 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
6c3bvpB_
99.8 27 PDB header:recombination
Chain: B: PDB Molecule:tp901-1 integrase;
PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase
7c3lhkA_
99.8 19 PDB header:dna binding protein
Chain: A: PDB Molecule:putative dna binding protein mj0014;
PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii.
8d2gm4a2
99.8 20 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
9c3lhfC_
99.8 23 PDB header:recombination
Chain: C: PDB Molecule:serine recombinase;
PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a
10c3pkzK_
99.7 23 PDB header:recombination
Chain: K: PDB Molecule:recombinase sin;
PDBTitle: structural basis for catalytic activation of a serine recombinase
11d2rsla_
99.7 24 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
12c3ploX_
99.7 25 PDB header:recombination
Chain: X: PDB Molecule:dna-invertase;
PDBTitle: crystal structure of the fis-independent mutant of gin
13d1hx7a_
99.5 23 Fold:Resolvase-like
Superfamily:Resolvase-like
Family:gamma,delta resolvase, catalytic domain
14c1u78A_
88.4 17 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
15c3cngC_
86.5 29 PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea
16c1i3qI_
83.8 15 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd
PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution
17c3ghgK_
80.4 8 PDB header:blood clotting
Chain: K: PDB Molecule:fibrinogen beta chain;
PDBTitle: crystal structure of human fibrinogen
18c1deqF_
76.5 10 PDB header:
PDB COMPND:
19c2gb5B_
73.3 20 PDB header:hydrolase
Chain: B: PDB Molecule:nadh pyrophosphatase;
PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution
20c2opfA_
72.2 22 PDB header:hydrolase/dna
Chain: A: PDB Molecule:endonuclease viii;
PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
21d1k78a2
not modelled 71.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
22c3h0gI_
not modelled 70.4 13 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
23c2k8dA_
not modelled 69.3 9 PDB header:oxidoreductase
Chain: A: PDB Molecule:peptide methionine sulfoxide reductase msrb;
PDBTitle: solution structure of a zinc-binding methionine sulfoxide reductase
24d2fiya1
not modelled 68.7 20 Fold:FdhE-like
Superfamily:FdhE-like
Family:FdhE-like
25c1k82D_
not modelled 68.7 13 PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna
26d6paxa2
not modelled 68.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
27d1k78a1
not modelled 68.1 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
28c1nnjA_
not modelled 65.6 14 PDB header:hydrolase
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna
29c1deqO_
not modelled 63.8 11 PDB header:
PDB COMPND:
30d2nlya1
not modelled 62.9 7 Fold:7-stranded beta/alpha barrel
Superfamily:Glycoside hydrolase/deacetylase
Family:Divergent polysaccharide deacetylase
31c2vrwB_
not modelled 62.8 14 PDB header:signaling protein
Chain: B: PDB Molecule:proto-oncogene vav;
PDBTitle: critical structural role for the ph and c1 domains of the2 vav1 exchange factor
32d1twfi1
not modelled 60.8 15 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
33d1pvma3
not modelled 60.4 21 Fold:Rubredoxin-like
Superfamily:Hypothetical protein Ta0289 C-terminal domain
Family:Hypothetical protein Ta0289 C-terminal domain
34d1wo8a1
not modelled 59.9 12 Fold:Methylglyoxal synthase-like
Superfamily:Methylglyoxal synthase-like
Family:Methylglyoxal synthase, MgsA
35d1dgsa1
59.1 20 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:NAD+-dependent DNA ligase, domain 3
36d1p91a_
not modelled 58.5 35 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:rRNA methyltransferase RlmA
37c2dq3A_
57.8 18 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: crystal structure of aq_298
38c2k27A_
not modelled 57.0 19 PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
39d1l1da_
not modelled 56.4 8 Fold:Mss4-like
Superfamily:Mss4-like
Family:SelR domain
40d1pdnc_
not modelled 55.9 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
41c1y1yS_
not modelled 55.4 12 PDB header:transferase/transcription/dna-rna hybrid
Chain: S: PDB Molecule:transcription elongation factor s-ii;
PDBTitle: rna polymerase ii-tfiis-dna/rna complex
42c3gn5B_
not modelled 55.4 13 PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
43d2g9wa1
not modelled 54.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
44c1pqvS_
not modelled 54.8 12 PDB header:transferase/transcription
Chain: S: PDB Molecule:transcription elongation factor s-ii;
PDBTitle: rna polymerase ii-tfiis complex
45c2f5qA_
not modelled 54.1 27 PDB header:hydrolase/dna
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase;
PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2
46d6paxa1
not modelled 53.7 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
47c2lcqA_
not modelled 53.0 19 PDB header:metal binding protein
Chain: A: PDB Molecule:putative toxin vapc6;
PDBTitle: solution structure of the endonuclease nob1 from p.horikoshii
48d1tfia_
not modelled 51.6 18 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
49d2iw0a1
not modelled 49.8 9 Fold:7-stranded beta/alpha barrel
Superfamily:Glycoside hydrolase/deacetylase
Family:NodB-like polysaccharide deacetylase
50c6paxA_
not modelled 48.8 21 PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
51d1dl6a_
not modelled 48.6 15 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
52c2krfB_
not modelled 48.3 27 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
53d1twfi2
not modelled 47.3 17 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
54c2riqA_
not modelled 47.0 19 PDB header:transferase
Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1;
PDBTitle: crystal structure of the third zinc-binding domain of human parp-1
55c3lssA_
not modelled 46.7 9 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: trypanosoma brucei seryl-trna synthetase in complex with atp
56d1yioa1
not modelled 46.3 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
57c3pfqA_
not modelled 46.0 26 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c beta type;
PDBTitle: crystal structure and allosteric activation of protein kinase c beta2 ii
58c3izci_
not modelled 45.6 16 PDB header:ribosome
Chain: I: PDB Molecule:60s ribosomal protein rpl10 (l10e);
PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
59c2jpcA_
not modelled 45.6 24 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
60c1ee8A_
not modelled 45.6 30 PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
61c2j6aA_
not modelled 45.1 26 PDB header:transferase
Chain: A: PDB Molecule:protein trm112;
PDBTitle: crystal structure of s. cerevisiae ynr046w, a zinc finger2 protein from the erf1 methyltransferase complex.
62c1zljE_
not modelled 45.0 15 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
63d1fsea_
not modelled 44.7 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
64c3hnwB_
not modelled 44.4 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a basic coiled-coil protein of unknown function2 from eubacterium eligens atcc 27750
65c3cezA_
not modelled 44.3 10 PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase;
PDBTitle: crystal structure of methionine-r-sulfoxide reductase from2 burkholderia pseudomallei
66d1p6ra_
not modelled 44.1 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
67c3hcjB_
not modelled 44.0 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:peptide methionine sulfoxide reductase;
PDBTitle: structure of msrb from xanthomonas campestris (oxidized2 form)
68c2l1uA_
not modelled 43.1 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase b2, mitochondrial;
PDBTitle: structure-functional analysis of mammalian msrb2 protein
69c2rnjA_
not modelled 42.3 21 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
70d1x6ma_
not modelled 41.5 33 Fold:Mss4-like
Superfamily:Mss4-like
Family:Glutathione-dependent formaldehyde-activating enzyme, Gfa
71c3fxaA_
not modelled 41.1 17 PDB header:sugar binding protein
Chain: A: PDB Molecule:sis domain protein;
PDBTitle: crystal structure of a putative sugar-phosphate isomerase2 (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 a3 resolution
72d1ivsa1
not modelled 40.9 16 Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Valyl-tRNA synthetase (ValRS) C-terminal domain
73d1xm0a1
not modelled 40.9 8 Fold:Mss4-like
Superfamily:Mss4-like
Family:SelR domain
74d1p4wa_
not modelled 40.9 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
75d1ny1a_
not modelled 40.1 11 Fold:7-stranded beta/alpha barrel
Superfamily:Glycoside hydrolase/deacetylase
Family:NodB-like polysaccharide deacetylase
76c2jeeA_
not modelled 39.9 18 PDB header:cell cycle
Chain: A: PDB Molecule:yiiu;
PDBTitle: xray structure of e. coli yiiu
77d1r2za3
not modelled 39.2 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
78d1ee8a3
not modelled 38.6 33 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
79d1l3la1
not modelled 38.4 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
80d2cona1
not modelled 38.2 36 Fold:Rubredoxin-like
Superfamily:NOB1 zinc finger-like
Family:NOB1 zinc finger-like
81c3dtpA_
not modelled 37.8 14 PDB header:contractile protein
Chain: A: PDB Molecule:myosin 2 heavy chain chimera of smooth and
PDBTitle: tarantula heavy meromyosin obtained by flexible docking to2 tarantula muscle thick filament cryo-em 3d-map
82c2jvmA_
not modelled 37.8 23 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution nmr structure of rhodobacter sphaeroides protein2 rhos4_26430. northeast structural genomics consortium3 target rhr95
83d1l1ta3
not modelled 37.6 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
84c2w48D_
not modelled 37.6 21 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
85d1qypa_
not modelled 37.2 30 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
86c2jvnA_
not modelled 37.1 19 PDB header:transferase
Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1;
PDBTitle: domain c of human parp-1
87d1sd4a_
not modelled 37.1 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
88d1tdza3
not modelled 37.0 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
89d1k82a3
not modelled 36.7 17 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
90d1pd0a5
not modelled 36.6 18 Fold:Rubredoxin-like
Superfamily:Zn-finger domain of Sec23/24
Family:Zn-finger domain of Sec23/24
91c3hugA_
not modelled 36.5 17 PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
92c3eg9B_
not modelled 35.8 15 PDB header:protein transport
Chain: B: PDB Molecule:sec24 related gene family, member d;
PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23/24 bound to the transport signal sequence of membrin
93d1x68a2
not modelled 35.8 40 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
94d1k3xa3
not modelled 35.3 33 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
95c2w3zA_
not modelled 35.2 6 PDB header:hydrolase
Chain: A: PDB Molecule:putative deacetylase;
PDBTitle: structure of a streptococcus mutans ce4 esterase
96c1w17A_
not modelled 35.0 11 PDB header:hydrolase
Chain: A: PDB Molecule:probable polysaccharide deacetylase pdaa;
PDBTitle: structure of bacillus subtilis pdaa, a family 42 carbohydrate esterase.
97d1tc3c_
not modelled 34.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
98c1ei3C_
not modelled 34.3 11 PDB header:
PDB COMPND:
99c3eh2B_
not modelled 34.2 12 PDB header:protein transport
Chain: B: PDB Molecule:protein transport protein sec24c;
PDBTitle: crystal structure of the human copii-coat protein sec24c
100d1ltla_
not modelled 33.9 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:DNA replication initiator (cdc21/cdc54) N-terminal domain
101c2gajA_
not modelled 33.7 18 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form
102d1ibia2
not modelled 33.6 17 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
103c2zq0B_
not modelled 33.1 6 PDB header:hydrolase
Chain: B: PDB Molecule:alpha-glucosidase (alpha-glucosidase susb);
PDBTitle: crystal structure of susb complexed with acarbose
104c3k7aM_
not modelled 32.6 24 PDB header:transcription
Chain: M: PDB Molecule:transcription initiation factor iib;
PDBTitle: crystal structure of an rna polymerase ii-tfiib complex
105c1ei3E_
not modelled 32.6 9 PDB header:
PDB COMPND:
106d1seta1
not modelled 32.5 18 Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Seryl-tRNA synthetase (SerRS)
107d2eppa1
not modelled 32.4 21 Fold:beta-beta-alpha zinc fingers
Superfamily:beta-beta-alpha zinc fingers
Family:Classic zinc finger, C2H2
108d1x94a_
not modelled 32.1 18 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
109d2dlda2
not modelled 32.0 21 Fold:Flavodoxin-like
Superfamily:Formate/glycerate dehydrogenase catalytic domain-like
Family:Formate/glycerate dehydrogenases, substrate-binding domain
110d1okra_
not modelled 31.8 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
111d2c71a1
not modelled 31.7 15 Fold:7-stranded beta/alpha barrel
Superfamily:Glycoside hydrolase/deacetylase
Family:NodB-like polysaccharide deacetylase
112c1x3uA_
not modelled 31.3 24 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
113c3bjiA_
not modelled 30.8 14 PDB header:signaling protein
Chain: A: PDB Molecule:proto-oncogene vav;
PDBTitle: structural basis of promiscuous guanine nucleotide exchange2 by the t-cell essential vav1
114c1m2vB_
not modelled 30.7 18 PDB header:protein transport
Chain: B: PDB Molecule:protein transport protein sec24;
PDBTitle: crystal structure of the yeast sec23/24 heterodimer
115d1gh9a_
not modelled 30.5 23 Fold:Rubredoxin-like
Superfamily:Hypothetical protein MTH1184
Family:Hypothetical protein MTH1184
116c3e0mB_
not modelled 30.5 8 PDB header:oxidoreductase
Chain: B: PDB Molecule:peptide methionine sulfoxide reductase msra/msrb
PDBTitle: crystal structure of fusion protein of msra and msrb
117d1vd4a_
not modelled 30.4 13 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
118c3u50C_
not modelled 30.1 14 PDB header:dna binding protein
Chain: C: PDB Molecule:telomerase-associated protein 82;
PDBTitle: crystal structure of the tetrahymena telomerase processivity factor2 teb1 ob-c
119d1m3sa_
not modelled 30.0 13 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
120c3egxB_
not modelled 30.0 13 PDB header:protein transport
Chain: B: PDB Molecule:protein transport protein sec24a;
PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23a/24a complexed with the snare protein sec22b and3 bound to the transport signal sequence of the snare protein4 bet1

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