Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP06972
DateThu Jan 5 10:59:37 GMT 2012
Unique Job IDc10a195fbc2cd4c0

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1l7va_
Top template information
Fold:ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily:ABC transporter involved in vitamin B12 uptake, BtuC
Family:ABC transporter involved in vitamin B12 uptake, BtuC
Confidence and coverage
Confidence:100.0% Coverage: 48%
314 residues ( 48% 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.
608 residues ( 92%) 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  MSKRIALFPALLLALLVIVATALTWMNFSQALPRSQWAQAAWSPDIDVIEQMIFHYSLLP
Secondary structure 
SS confidence 
Disorder  ?????
????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  RLAISLLVGAGLGLVGVLFQQVLRNPLAEPTTLGVATGAQLGITVTTLWAIPGAMASQFA
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  AQAGACVVGLIVFGVAWGKRLSPVTLILAGLVVSLYCGAINQLLVIFHHDQLQSMFLWST
Secondary structure 
SS confidence 
Disorder 
?
????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  GTLTQTDWGGVERLWPQLLGGVMLTLLLLRPLTLMGLDDGVARNLGLALSLARLAALSLA
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  IVISALLVNAVGIIGFIGLFAPLLAKMLGARRLLPRLMLASLIGALILWLSDQIILWLTR
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  VWMEVSTGSVTALIGAPLLLWLLPRLRSISAPDMKVNDRVAAERQHVLAFALAGGVLLLM
Secondary structure 
SS confidence 
Disorder  ?
??????????????????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  AVVVALSFGRDAHGWTWASGALLEDLMPWRWPRIMAALFAGVMLAVAGCIIQRLTGNPMA
Secondary structure 
SS confidence 
Disorder 
?
??????
??
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  SPEVLGISSGAAFGVVLMLFLVPGNAFGWLLPAGSLGAAVTLLIIMIAAGRGGFSPHRML
Secondary structure 
SS confidence 
Disorder 
??
????
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  LAGMALSTAFTMLLMMLQASGDPRMAQVLTWISGSTYNATDAQVWRTGIVMVILLAITPL
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  CRRWLTILPLGGDTARAVGMALTPTRIALLLLAACLTATATMTIGPLSFVGLMAPHIARM
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  MGFRRTMPHIVISALVGGLLLVFADWCGRMVLFPFQIPAGLLSTFIGAPYFIYLLRKQSR
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
  
Sequence 
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 1l7v chain A

3D model

Region: 2 - 325
Aligned: 314
Modelled: 324
Confidence: 100.0%
Identity: 27%
Fold: ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily: ABC transporter involved in vitamin B12 uptake, BtuC
Family: ABC transporter involved in vitamin B12 uptake, BtuC

Phyre2

PDB 2nq2 chain A

3D model

Region: 347 - 657
Aligned: 305
Modelled: 311
Confidence: 100.0%
Identity: 27%
PDB header:metal transport
Chain: A: PDB Molecule:hypothetical abc transporter permease protein
PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter.

Phyre2

PDB 1ots chain A

3D model

Region: 138 - 485
Aligned: 339
Modelled: 348
Confidence: 51.2%
Identity: 11%
Fold: Clc chloride channel
Superfamily: Clc chloride channel
Family: Clc chloride channel

Phyre2

PDB 1kpl chain A

3D model

Region: 142 - 485
Aligned: 335
Modelled: 337
Confidence: 46.2%
Identity: 14%
Fold: Clc chloride channel
Superfamily: Clc chloride channel
Family: Clc chloride channel

Phyre2

PDB 3k3g chain A

3D model

Region: 60 - 346
Aligned: 264
Modelled: 266
Confidence: 38.0%
Identity: 11%
PDB header:transport protein
Chain: A: PDB Molecule:urea transporter;
PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea

Phyre2

PDB 1yce chain D

3D model

Region: 74 - 115
Aligned: 42
Modelled: 42
Confidence: 27.6%
Identity: 14%
PDB header:membrane protein
Chain: D: PDB Molecule:subunit c;
PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus

Phyre2

PDB 1q1h chain A

3D model

Region: 551 - 572
Aligned: 22
Modelled: 22
Confidence: 22.2%
Identity: 23%
PDB header:transcription
Chain: A: PDB Molecule:transcription factor e;
PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha

Phyre2

PDB 1q1h chain A

3D model

Region: 551 - 572
Aligned: 22
Modelled: 22
Confidence: 22.2%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Transcription factor E/IIe-alpha, N-terminal domain

Phyre2

PDB 2ht2 chain B

3D model

Region: 138 - 485
Aligned: 335
Modelled: 348
Confidence: 20.9%
Identity: 12%
PDB header:membrane protein
Chain: B: PDB Molecule:h(+)/cl(-) exchange transporter clca;
PDBTitle: structure of the escherichia coli clc chloride channel2 y445h mutant and fab complex

Phyre2

PDB 2w5j chain M

3D model

Region: 74 - 114
Aligned: 41
Modelled: 41
Confidence: 18.6%
Identity: 20%
PDB header:hydrolase
Chain: M: PDB Molecule:atp synthase c chain, chloroplastic;
PDBTitle: structure of the c14-rotor ring of the proton translocating2 chloroplast atp synthase

Phyre2

PDB 2xnd chain K

3D model

Region: 74 - 111
Aligned: 38
Modelled: 38
Confidence: 17.5%
Identity: 21%
PDB header:hydrolase
Chain: K: PDB Molecule:atp synthase lipid-binding protein, mitochondrial;
PDBTitle: crystal structure of bovine f1-c8 sub-complex of atp2 synthase

Phyre2

PDB 2p7t chain C domain 1

3D model

Region: 244 - 273
Aligned: 29
Modelled: 30
Confidence: 16.6%
Identity: 34%
Fold: Voltage-gated potassium channels
Superfamily: Voltage-gated potassium channels
Family: Voltage-gated potassium channels

Phyre2

PDB 3lrc chain C

3D model

Region: 470 - 660
Aligned: 183
Modelled: 191
Confidence: 15.3%
Identity: 7%
PDB header:transport protein
Chain: C: PDB Molecule:arginine/agmatine antiporter;
PDBTitle: structure of e. coli adic (p1)

Phyre2

PDB 2b2h chain A

3D model

Region: 310 - 562
Aligned: 218
Modelled: 237
Confidence: 15.3%
Identity: 13%
PDB header:transport protein
Chain: A: PDB Molecule:ammonium transporter;
PDBTitle: ammonium transporter amt-1 from a. fulgidus (as)

Phyre2

PDB 2wpd chain P

3D model

Region: 74 - 112
Aligned: 39
Modelled: 39
Confidence: 14.5%
Identity: 23%
PDB header:hydrolase
Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial;
PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase

Phyre2

PDB 3qnq chain D

3D model

Region: 518 - 561
Aligned: 44
Modelled: 44
Confidence: 14.4%
Identity: 7%
PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system

Phyre2

PDB 2r5f chain A domain 1

3D model

Region: 200 - 226
Aligned: 27
Modelled: 27
Confidence: 13.5%
Identity: 33%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: SorC sugar-binding domain-like

Phyre2

PDB 2knc chain A

3D model

Region: 447 - 474
Aligned: 28
Modelled: 28
Confidence: 12.3%
Identity: 32%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2

PDB 2x2v chain G

3D model

Region: 74 - 111
Aligned: 38
Modelled: 38
Confidence: 12.0%
Identity: 18%
PDB header:membrane protein
Chain: G: PDB Molecule:atp synthase subunit c;
PDBTitle: structural basis of a novel proton-coordination type in an2 f1fo-atp synthase rotor ring

Phyre2

PDB 1y88 chain A domain 1

3D model

Region: 213 - 236
Aligned: 24
Modelled: 24
Confidence: 11.6%
Identity: 21%
Fold: SAM domain-like
Superfamily: Rad51 N-terminal domain-like
Family: Hypothetical protein AF1548, C-terminal domain

Phyre2
1
d1l7va_
2
c2nq2A_
3
d1otsa_
4
d1kpla_
5
c3k3gA_
6
c1yceD_
7
c1q1hA_
8
d1q1ha_
9
c2ht2B_
10
c2w5jM_
11
c2xndK_
12
d2p7tc1
13
c3lrcC_
14
c2b2hA_
15
c2wpdP_
16
c3qnqD_
17
d2r5fa1
18
c2kncA_
19
c2x2vG_
20
d1y88a1
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1l7va_
100.0 27 Fold:ABC transporter involved in vitamin B12 uptake, BtuC
Superfamily:ABC transporter involved in vitamin B12 uptake, BtuC
Family:ABC transporter involved in vitamin B12 uptake, BtuC
2c2nq2A_
100.0 27 PDB header:metal transport
Chain: A: PDB Molecule:hypothetical abc transporter permease protein
PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter.
3d1otsa_
51.2 11 Fold:Clc chloride channel
Superfamily:Clc chloride channel
Family:Clc chloride channel
4d1kpla_
46.2 14 Fold:Clc chloride channel
Superfamily:Clc chloride channel
Family:Clc chloride channel
5c3k3gA_
38.0 11 PDB header:transport protein
Chain: A: PDB Molecule:urea transporter;
PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea
6c1yceD_
27.6 14 PDB header:membrane protein
Chain: D: PDB Molecule:subunit c;
PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus
7c1q1hA_
22.2 23 PDB header:transcription
Chain: A: PDB Molecule:transcription factor e;
PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha
8d1q1ha_
22.2 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcription factor E/IIe-alpha, N-terminal domain
9c2ht2B_
20.9 12 PDB header:membrane protein
Chain: B: PDB Molecule:h(+)/cl(-) exchange transporter clca;
PDBTitle: structure of the escherichia coli clc chloride channel2 y445h mutant and fab complex
10c2w5jM_
18.6 20 PDB header:hydrolase
Chain: M: PDB Molecule:atp synthase c chain, chloroplastic;
PDBTitle: structure of the c14-rotor ring of the proton translocating2 chloroplast atp synthase
11c2xndK_
17.5 21 PDB header:hydrolase
Chain: K: PDB Molecule:atp synthase lipid-binding protein, mitochondrial;
PDBTitle: crystal structure of bovine f1-c8 sub-complex of atp2 synthase
12d2p7tc1
16.6 34 Fold:Voltage-gated potassium channels
Superfamily:Voltage-gated potassium channels
Family:Voltage-gated potassium channels
13c3lrcC_
15.3 7 PDB header:transport protein
Chain: C: PDB Molecule:arginine/agmatine antiporter;
PDBTitle: structure of e. coli adic (p1)
14c2b2hA_
15.3 13 PDB header:transport protein
Chain: A: PDB Molecule:ammonium transporter;
PDBTitle: ammonium transporter amt-1 from a. fulgidus (as)
15c2wpdP_
14.5 23 PDB header:hydrolase
Chain: P: PDB Molecule:atp synthase subunit 9, mitochondrial;
PDBTitle: the mg.adp inhibited state of the yeast f1c10 atp synthase
16c3qnqD_
14.4 7 PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
17d2r5fa1
13.5 33 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:SorC sugar-binding domain-like
18c2kncA_
12.3 32 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
19c2x2vG_
12.0 18 PDB header:membrane protein
Chain: G: PDB Molecule:atp synthase subunit c;
PDBTitle: structural basis of a novel proton-coordination type in an2 f1fo-atp synthase rotor ring
20d1y88a1
11.6 21 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:Hypothetical protein AF1548, C-terminal domain
21c2zt9E_
not modelled 11.5 34 PDB header:photosynthesis
Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6;
PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120
22c2o012_
not modelled 11.2 48 PDB header:photosynthesis
Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
23c3a03A_
not modelled 11.1 11 PDB header:gene regulation
Chain: A: PDB Molecule:t-cell leukemia homeobox protein 2;
PDBTitle: crystal structure of hox11l1 homeodomain
24c2jd3B_
not modelled 10.8 33 PDB header:dna binding protein
Chain: B: PDB Molecule:stbb protein;
PDBTitle: parr from plasmid pb171
25d1du0a_
not modelled 10.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
26d1x2ma1
not modelled 10.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
27c3mk7F_
not modelled 10.5 11 PDB header:oxidoreductase
Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p;
PDBTitle: the structure of cbb3 cytochrome oxidase
28c2kfsA_
not modelled 10.4 28 PDB header:dna-binding protein
Chain: A: PDB Molecule:conserved hypothetical regulatory protein;
PDBTitle: nmr structure of rv2175c
29d1ku2a1
not modelled 10.4 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
30d1rh5b_
not modelled 10.3 33 Fold:Single transmembrane helix
Superfamily:Preprotein translocase SecE subunit
Family:Preprotein translocase SecE subunit
31c1iijA_
not modelled 10.0 35 PDB header:signaling protein
Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase;
PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment
32c2vi6F_
not modelled 9.6 11 PDB header:transcription
Chain: F: PDB Molecule:homeobox protein nanog;
PDBTitle: crystal structure of the nanog homeodomain
33c1l0oC_
not modelled 9.6 28 PDB header:protein binding
Chain: C: PDB Molecule:sigma factor;
PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf
34d1l0oc_
not modelled 9.6 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
35c3cmwA_
not modelled 9.5 27 PDB header:recombination/dna
Chain: A: PDB Molecule:protein reca;
PDBTitle: mechanism of homologous recombination from the reca-2 ssdna/dsdna structures
36d2p7vb1
not modelled 9.4 12 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
37c2da4A_
not modelled 9.4 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein dkfzp686k21156;
PDBTitle: solution structure of the homeobox domain of the2 hypothetical protein, dkfzp686k21156
38c1fftG_
not modelled 9.4 5 PDB header:oxidoreductase
Chain: G: PDB Molecule:ubiquinol oxidase;
PDBTitle: the structure of ubiquinol oxidase from escherichia coli
39c2xglB_
not modelled 9.3 18 PDB header:antibiotic
Chain: B: PDB Molecule:colicin-m immunity protein;
PDBTitle: the x-ray structure of the escherichia coli colicin m immunity2 protein demonstrates the presence of a disulphide bridge, which is3 functionally essential
40c3nd0A_
not modelled 9.3 10 PDB header:transport protein
Chain: A: PDB Molecule:sll0855 protein;
PDBTitle: x-ray crystal structure of a slow cyanobacterial cl-/h+ antiporter
41c2jwaA_
not modelled 9.3 18 PDB header:transferase
Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2;
PDBTitle: erbb2 transmembrane segment dimer spatial structure
42d1rp3a1
not modelled 9.3 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
43d1akha_
not modelled 9.2 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
44d1sana_
not modelled 9.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
45c1yi7C_
not modelled 8.9 31 PDB header:hydrolase
Chain: C: PDB Molecule:beta-xylosidase, family 43 glycosyl hydrolase;
PDBTitle: beta-d-xylosidase (selenomethionine) xynd from clostridium2 acetobutylicum
46d1ku3a_
not modelled 8.9 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
47c3aqpB_
not modelled 8.8 21 PDB header:membrane protein
Chain: B: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus
48c2kz3A_
not modelled 8.8 24 PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein rad51l3;
PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for human rad51d2 from 1 to 83
49d2o34a1
not modelled 8.7 20 Fold:T-fold
Superfamily:ApbE-like
Family:DVU1097-like
50c1wu0A_
not modelled 8.5 22 PDB header:hydrolase
Chain: A: PDB Molecule:atp synthase c chain;
PDBTitle: solution structure of subunit c of f1fo-atp synthase from2 the thermophilic bacillus ps3
51d1wh5a_
not modelled 8.5 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
52d1le8a_
not modelled 8.5 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
53d1ttya_
not modelled 8.4 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
54d1p7ia_
not modelled 8.4 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
55d2p81a1
not modelled 8.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
56c3t72o_
not modelled 8.3 12 PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex
57d2asba2
not modelled 8.2 29 Fold:Alpha-lytic protease prodomain-like
Superfamily:Prokaryotic type KH domain (KH-domain type II)
Family:Prokaryotic type KH domain (KH-domain type II)
58c3k69A_
not modelled 8.2 19 PDB header:transcription
Chain: A: PDB Molecule:putative transcription regulator;
PDBTitle: crystal structure of a putative transcriptional regulator (lp_0360)2 from lactobacillus plantarum at 1.95 a resolution
59c2da7A_
not modelled 8.2 11 PDB header:dna binding protein
Chain: A: PDB Molecule:zinc finger homeobox protein 1b;
PDBTitle: solution structure of the homeobox domain of zinc finger2 homeobox protein 1b (smad interacting protein 1)
60c2xvtC_
not modelled 8.2 42 PDB header:membrane protein
Chain: C: PDB Molecule:receptor activity-modifying protein 2;
PDBTitle: structure of the extracellular domain of human ramp2
61c2k1aA_
not modelled 8.2 32 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment
62d1b8ia_
not modelled 8.1 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
63c2jmlA_
not modelled 8.1 25 PDB header:transcription
Chain: A: PDB Molecule:dna binding domain/transcriptional regulator;
PDBTitle: solution structure of the n-terminal domain of cara repressor
64d1rhzb_
not modelled 8.0 24 Fold:Single transmembrane helix
Superfamily:Preprotein translocase SecE subunit
Family:Preprotein translocase SecE subunit
65d1mylb_
not modelled 8.0 38 Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:Arc/Mnt-like phage repressors
66d1o4xa1
not modelled 7.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
67d1ku7a_
not modelled 7.9 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
68d1rc2a_
not modelled 7.9 26 Fold:Aquaporin-like
Superfamily:Aquaporin-like
Family:Aquaporin-like
69c2djnA_
not modelled 7.9 22 PDB header:transcription
Chain: A: PDB Molecule:homeobox protein dlx-5;
PDBTitle: the solution structure of the homeobox domain of human2 homeobox protein dlx-5
70d1bw5a_
not modelled 7.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
71d1f43a_
not modelled 7.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
72c2rn7A_
not modelled 7.7 17 PDB header:unknown function
Chain: A: PDB Molecule:is629 orfa;
PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125
73c2l2tA_
not modelled 7.7 24 PDB header:membrane protein
Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4;
PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain
74c2o8xA_
not modelled 7.7 17 PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
75c2k40A_
not modelled 7.6 22 PDB header:dna binding protein
Chain: A: PDB Molecule:homeobox expressed in es cells 1;
PDBTitle: nmr structure of hesx-1 homeodomain double mutant r31l/e42l
76c3cmuA_
not modelled 7.6 24 PDB header:recombination/dna
Chain: A: PDB Molecule:protein reca;
PDBTitle: mechanism of homologous recombination from the reca-2 ssdna/dsdna structures
77d1f6ga_
not modelled 7.6 28 Fold:Voltage-gated potassium channels
Superfamily:Voltage-gated potassium channels
Family:Voltage-gated potassium channels
78d1pufa_
not modelled 7.6 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
79d1s7ea1
not modelled 7.6 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
80d1b72a_
not modelled 7.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
81c2kv5A_
not modelled 7.6 20 PDB header:toxin
Chain: A: PDB Molecule:putative uncharacterized protein rnai;
PDBTitle: solution structure of the par toxin fst in dpc micelles
82d2craa1
not modelled 7.5 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
83d1zq3p1
not modelled 7.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
84c2x48B_
not modelled 7.5 22 PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
85d2hi3a1
not modelled 7.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
86c3u5eL_
not modelled 7.4 26 PDB header:ribosome
Chain: L: PDB Molecule:60s ribosomal protein l13-a;
PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution
87c2wwbB_
not modelled 7.4 28 PDB header:ribosome
Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma;
PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome
88c3a01A_
not modelled 7.3 17 PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeodomain-containing protein;
PDBTitle: crystal structure of aristaless and clawless homeodomains bound to dna
89d1s9ca1
not modelled 7.3 15 Fold:Thioesterase/thiol ester dehydrase-isomerase
Superfamily:Thioesterase/thiol ester dehydrase-isomerase
Family:MaoC-like
90d1l8qa1
not modelled 7.3 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Chromosomal replication initiation factor DnaA C-terminal domain IV
91d1js2a_
not modelled 7.3 25 Fold:HIPIP (high potential iron protein)
Superfamily:HIPIP (high potential iron protein)
Family:HIPIP (high potential iron protein)
92c2yx8A_
not modelled 7.3 25 PDB header:protein transport
Chain: A: PDB Molecule:receptor activity-modifying protein 1;
PDBTitle: crystal structure of the extracellular domain of human ramp1
93d1ocpa_
not modelled 7.3 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
94d1myka_
not modelled 7.3 38 Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:Arc/Mnt-like phage repressors
95d1smyf2
not modelled 7.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
96c4a18U_
not modelled 7.2 21 PDB header:ribosome
Chain: U: PDB Molecule:rpl13;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1
97d1yz8p1
not modelled 7.2 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Homeodomain
98d2dt5a1
not modelled 7.1 6 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional repressor Rex, N-terminal domain
99c2dmsA_
not modelled 7.1 22 PDB header:dna binding protein
Chain: A: PDB Molecule:homeobox protein otx2;
PDBTitle: solution structure of the homeobox domain of homeobox2 protein otx2

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