Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ00037
DateThu Jan 5 12:33:19 GMT 2012
Unique Job ID6b36dd0132f99367

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1x5bA_
Top template information
PDB header:protein binding
Chain: A: PDB Molecule:signal transducing adaptor molecule 2;
PDBTitle: the solution structure of the vhs domain of human signal2 transducing adaptor molecule 2
Confidence and coverage
Confidence: 75.9% Coverage: 14%
136 residues ( 14% of your sequence) have been modelled with 75.9% 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.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MPVDFLTSDQKQNYGCYAAEPNDVQLARYFHLDERDLAFINQRRGKHNRLGIALQLTTAR
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Disorder  ???????




















































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   .........70.........80.........90.........100.........110.........120
Sequence  FLGTFLTDLTQVLPGVQHFVAVQLNIHRPEVLSRYAERDTTLREHTALIKEYYGYHEFGD
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????


















?
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   .........130.........140.........150.........160.........170.........180
Sequence  FPWSFRLKRLLYTRAWLSNERPGLMFDFATAWLLQNKVLLPGATTLVRLISEIRERANQR
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   .........190.........200.........210.........220.........230.........240
Sequence  LWKKLAALPNKWQAAQVMELLVIPEGQRVSALEQLKKGPVTVSGPAFNEALERYIRLRSL
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??








?
?
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   .........250.........260.........270.........280.........290.........300
Sequence  EFSRLNFSGLPAIQLRNLARYAGMASVKYIARMPQQRKLAVLTAFVKAQEITALDDAVDV
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?























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   .........310.........320.........330.........340.........350.........360
Sequence  LDMLILDIIREAKKTGQKKRLRTLKDLDQAALLLARACALLLDDNTDVPDLRQVIFKCVP
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   .........370.........380.........390.........400.........410.........420
Sequence  KNRLAESVSKVNELARPQNNNFHDEMVEQYGRVKRFLPAVLRDLHFRAAPAGEHVLAAIH
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   .........430.........440.........450.........460.........470.........480
Sequence  YLAELNGSKKRILDDAPEHIITGPWKRLVYDAEGRIQRAGYSLCLLERLQDALRRRDIWL
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   .........490.........500.........510.........520.........530.........540
Sequence  ENSDRWGDPREKLLQGEEWQTQRIPVCRALGHPVDGRKGVQQLAIQLDETWKAVASRFEK
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   .........550.........560.........570.........580.........590.........600
Sequence  NAEVHICNEGKYPSLTISCLEKQEEPPSLLRLNNRIKQLLPPVDLTELLLEIDAQTGFTH
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Disorder 
???
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   .........610.........620.........630.........640.........650.........660
Sequence  EFAHVSESGARAQDLHISLCAVLMAEACNIGLEPLIKHNIPALTRHRLSWVKQNYLRAET
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???????????




















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   .........670.........680.........690.........700.........710.........720
Sequence  LVSANARLVDFQSTLELAGRWGGGEVASADGMRFVTPVKTINSGSNRKYFGSGRGITWYN
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   .........730.........740.........750.........760.........770.........780
Sequence  FVSDQYSGFHGIVVPGTLRDSIFVLEGLLEQQTGLNPVEIMTDTAGSSDIIFGLFWLLGY
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   .........790.........800.........810.........820.........830.........840
Sequence  QFSPRLADAGEAVFWRVNKSANYGVLDKLARGYADLSKAESQWDEMMRTAGSLKLGTIHA
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   .........850.........860.........870.........880.........890.........900
Sequence  SELIRSLLKSSRPSGLAQAIMEVGRVNKTLYLLNYIDDEDYRRRILTQLNRGEGRHAVAR
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   .........910.........920.........930.........940.........950.........960
Sequence  AICYGQRGEIRKRYREGQEDQLGALGLVTNAVVLWNTLYMEEALSWMRRNGEEIIDEDIA
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   .........970.........980.........990.........1000..
Sequence  RLSPLMHGHINMLGHYTFTLPEDILKGELRALNLNINNELSP
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??????????





???????
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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 1x5b chain A

3D model

Region: 805 - 964
Aligned: 136
Modelled: 137
Confidence: 75.9%
Identity: 10%
PDB header:protein binding
Chain: A: PDB Molecule:signal transducing adaptor molecule 2;
PDBTitle: the solution structure of the vhs domain of human signal2 transducing adaptor molecule 2

Phyre2

PDB 1dvp chain A domain 1

3D model

Region: 805 - 956
Aligned: 131
Modelled: 132
Confidence: 61.5%
Identity: 9%
Fold: alpha-alpha superhelix
Superfamily: ENTH/VHS domain
Family: VHS domain

Phyre2

PDB 3zyq chain A

3D model

Region: 804 - 956
Aligned: 128
Modelled: 153
Confidence: 47.8%
Identity: 17%
PDB header:signaling
Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase
PDBTitle: crystal structure of the tandem vhs and fyve domains of hepatocyte2 growth factor-regulated tyrosine kinase substrate (hgs-hrs) at 1.483 a resolution

Phyre2

PDB 1elk chain A

3D model

Region: 799 - 955
Aligned: 137
Modelled: 157
Confidence: 42.7%
Identity: 10%
Fold: alpha-alpha superhelix
Superfamily: ENTH/VHS domain
Family: VHS domain

Phyre2

PDB 2ezh chain A

3D model

Region: 138 - 173
Aligned: 36
Modelled: 36
Confidence: 42.5%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Recombinase DNA-binding domain

Phyre2

PDB 2w36 chain B

3D model

Region: 739 - 780
Aligned: 40
Modelled: 42
Confidence: 40.1%
Identity: 20%
PDB header:hydrolase
Chain: B: PDB Molecule:endonuclease v;
PDBTitle: structures of endonuclease v with dna reveal initiation of2 deaminated adenine repair

Phyre2

PDB 3i26 chain C

3D model

Region: 690 - 758
Aligned: 68
Modelled: 69
Confidence: 39.9%
Identity: 22%
PDB header:hydrolase
Chain: C: PDB Molecule:hemagglutinin-esterase;
PDBTitle: structure of bovine torovirus hemagglutinin-esterase

Phyre2

PDB 1ujk chain A

3D model

Region: 798 - 952
Aligned: 139
Modelled: 155
Confidence: 37.9%
Identity: 12%
Fold: alpha-alpha superhelix
Superfamily: ENTH/VHS domain
Family: VHS domain

Phyre2

PDB 3onl chain B

3D model

Region: 821 - 930
Aligned: 97
Modelled: 110
Confidence: 37.1%
Identity: 14%
PDB header:protein transport
Chain: B: PDB Molecule:epsin-3;
PDBTitle: yeast ent3_enth-vti1p_habc complex structure

Phyre2

PDB 3goc chain B

3D model

Region: 739 - 780
Aligned: 40
Modelled: 42
Confidence: 36.9%
Identity: 33%
PDB header:hydrolase
Chain: B: PDB Molecule:endonuclease v;
PDBTitle: crystal structure of the endonuclease v (sav1684) from streptomyces2 avermitilis. northeast structural genomics consortium target svr196

Phyre2

PDB 3ga2 chain A

3D model

Region: 739 - 780
Aligned: 40
Modelled: 42
Confidence: 36.9%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:endonuclease v;
PDBTitle: crystal structure of the endonuclease_v (bsu36170) from2 bacillus subtilis, northeast structural genomics3 consortium target sr624

Phyre2

PDB 1oz9 chain A

3D model

Region: 770 - 781
Aligned: 12
Modelled: 12
Confidence: 34.1%
Identity: 50%
Fold: Zincin-like
Superfamily: Metalloproteases ("zincins"), catalytic domain
Family: Predicted metal-dependent hydrolase

Phyre2

PDB 2ezi chain A

3D model

Region: 126 - 183
Aligned: 57
Modelled: 58
Confidence: 33.5%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Recombinase DNA-binding domain

Phyre2

PDB 2r18 chain A

3D model

Region: 22 - 71
Aligned: 45
Modelled: 50
Confidence: 31.5%
Identity: 11%
PDB header:viral protein
Chain: A: PDB Molecule:capsid assembly protein vp3;
PDBTitle: structural insights into the multifunctional protein vp3 of2 birnaviruses

Phyre2

PDB 1xm5 chain A

3D model

Region: 770 - 781
Aligned: 12
Modelled: 12
Confidence: 31.1%
Identity: 42%
Fold: Zincin-like
Superfamily: Metalloproteases ("zincins"), catalytic domain
Family: Predicted metal-dependent hydrolase

Phyre2

PDB 1tvi chain A

3D model

Region: 770 - 781
Aligned: 12
Modelled: 12
Confidence: 30.3%
Identity: 42%
Fold: Zincin-like
Superfamily: Metalloproteases ("zincins"), catalytic domain
Family: Predicted metal-dependent hydrolase

Phyre2

PDB 1dp7 chain P

3D model

Region: 845 - 871
Aligned: 25
Modelled: 27
Confidence: 29.3%
Identity: 8%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: P4 origin-binding domain-like

Phyre2

PDB 1cy5 chain A

3D model

Region: 6 - 89
Aligned: 84
Modelled: 84
Confidence: 28.9%
Identity: 7%
Fold: DEATH domain
Superfamily: DEATH domain
Family: Caspase recruitment domain, CARD

Phyre2

PDB 1xax chain A

3D model

Region: 770 - 781
Aligned: 12
Modelled: 12
Confidence: 27.1%
Identity: 42%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical upf0054 protein hi0004;
PDBTitle: nmr structure of hi0004, a putative essential gene product2 from haemophilus influenzae

Phyre2

PDB 3sqg chain E

3D model

Region: 705 - 736
Aligned: 30
Modelled: 32
Confidence: 23.1%
Identity: 27%
PDB header:transferase
Chain: E: PDB Molecule:methyl-coenzyme m reductase, beta subunit;
PDBTitle: crystal structure of a methyl-coenzyme m reductase purified from black2 sea mats

Phyre2
1

c1x5bA_
2

d1dvpa1
3

c3zyqA_
4

d1elka_
5

d2ezha_
6

c2w36B_
7

c3i26C_
8

d1ujka_
9

c3onlB_
10

c3gocB_
11

c3ga2A_
12

d1oz9a_
13

d2ezia_
14

c2r18A_
15

d1xm5a_
16

d1tvia_
17

d1dp7p_
18

d1cy5a_
19

c1xaxA_
20

c3sqgE_
21



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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1x5bA_



75.9 10 PDB header:protein binding
Chain: A: PDB Molecule:signal transducing adaptor molecule 2;
PDBTitle: the solution structure of the vhs domain of human signal2 transducing adaptor molecule 2
2d1dvpa1



61.5 9 Fold:alpha-alpha superhelix
Superfamily:ENTH/VHS domain
Family:VHS domain
3c3zyqA_



47.8 17 PDB header:signaling
Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase
PDBTitle: crystal structure of the tandem vhs and fyve domains of hepatocyte2 growth factor-regulated tyrosine kinase substrate (hgs-hrs) at 1.483 a resolution
4d1elka_



42.7 10 Fold:alpha-alpha superhelix
Superfamily:ENTH/VHS domain
Family:VHS domain
5d2ezha_



42.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
6c2w36B_



40.1 20 PDB header:hydrolase
Chain: B: PDB Molecule:endonuclease v;
PDBTitle: structures of endonuclease v with dna reveal initiation of2 deaminated adenine repair
7c3i26C_



39.9 22 PDB header:hydrolase
Chain: C: PDB Molecule:hemagglutinin-esterase;
PDBTitle: structure of bovine torovirus hemagglutinin-esterase
8d1ujka_



37.9 12 Fold:alpha-alpha superhelix
Superfamily:ENTH/VHS domain
Family:VHS domain
9c3onlB_



37.1 14 PDB header:protein transport
Chain: B: PDB Molecule:epsin-3;
PDBTitle: yeast ent3_enth-vti1p_habc complex structure
10c3gocB_



36.9 33 PDB header:hydrolase
Chain: B: PDB Molecule:endonuclease v;
PDBTitle: crystal structure of the endonuclease v (sav1684) from streptomyces2 avermitilis. northeast structural genomics consortium target svr196
11c3ga2A_



36.9 18 PDB header:hydrolase
Chain: A: PDB Molecule:endonuclease v;
PDBTitle: crystal structure of the endonuclease_v (bsu36170) from2 bacillus subtilis, northeast structural genomics3 consortium target sr624
12d1oz9a_



34.1 50 Fold:Zincin-like
Superfamily:Metalloproteases ("zincins"), catalytic domain
Family:Predicted metal-dependent hydrolase
13d2ezia_



33.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
14c2r18A_



31.5 11 PDB header:viral protein
Chain: A: PDB Molecule:capsid assembly protein vp3;
PDBTitle: structural insights into the multifunctional protein vp3 of2 birnaviruses
15d1xm5a_



31.1 42 Fold:Zincin-like
Superfamily:Metalloproteases ("zincins"), catalytic domain
Family:Predicted metal-dependent hydrolase
16d1tvia_



30.3 42 Fold:Zincin-like
Superfamily:Metalloproteases ("zincins"), catalytic domain
Family:Predicted metal-dependent hydrolase
17d1dp7p_



29.3 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:P4 origin-binding domain-like
18d1cy5a_



28.9 7 Fold:DEATH domain
Superfamily:DEATH domain
Family:Caspase recruitment domain, CARD
19c1xaxA_



27.1 42 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical upf0054 protein hi0004;
PDBTitle: nmr structure of hi0004, a putative essential gene product2 from haemophilus influenzae
20c3sqgE_



23.1 27 PDB header:transferase
Chain: E: PDB Molecule:methyl-coenzyme m reductase, beta subunit;
PDBTitle: crystal structure of a methyl-coenzyme m reductase purified from black2 sea mats
21d1t1ua2



not modelled 22.0 19 Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:Choline/Carnitine O-acyltransferase
22c2eqoA_



not modelled 21.9 24 PDB header:transcription
Chain: A: PDB Molecule:tnf receptor-associated factor 3-interacting
PDBTitle: solution structure of the stn_traf3ip1_nd domain of2 interleukin 13 receptor alpha 1-binding protein-1 [homo3 sapiens]
23d1dmga_



not modelled 21.2 14 Fold:Ribosomal protein L4
Superfamily:Ribosomal protein L4
Family:Ribosomal protein L4
24c3pvlA_



not modelled 20.5 14 PDB header:motor protein/protein transport
Chain: A: PDB Molecule:myosin viia isoform 1;
PDBTitle: structure of myosin viia myth4-ferm-sh3 in complex with the cen1 of2 sans
25c3ghgK_



not modelled 20.0 31 PDB header:blood clotting
Chain: K: PDB Molecule:fibrinogen beta chain;
PDBTitle: crystal structure of human fibrinogen
26d2opla1



not modelled 19.5 19 Fold:OsmC-like
Superfamily:OsmC-like
Family:Ohr/OsmC resistance proteins
27d1ndba2



not modelled 19.3 20 Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:Choline/Carnitine O-acyltransferase
28c1h0mD_



not modelled 19.2 10 PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna
29c1zljE_



not modelled 19.0 7 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
30c1hbmE_



not modelled 18.0 33 PDB header:methanogenesis
Chain: E: PDB Molecule:methyl-coenzyme m reductase i beta subunit;
PDBTitle: methyl-coenzyme m reductase enzyme product complex
31c3edeB_



not modelled 18.0 14 PDB header:hydrolase
Chain: B: PDB Molecule:cyclomaltodextrinase;
PDBTitle: structural base for cyclodextrin hydrolysis
32d1a04a1



not modelled 17.9 13 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)
33d1h3ga3



not modelled 17.8 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
34d1hbnb1



not modelled 17.7 33 Fold:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
35c2vgqA_



not modelled 17.3 19 PDB header:immune system/transport
Chain: A: PDB Molecule:maltose-binding periplasmic protein,
PDBTitle: crystal structure of human ips-1 card
36c1deqO_



not modelled 17.2 33 PDB header:
PDB COMPND:
37d1nm8a2



not modelled 17.0 20 Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:Choline/Carnitine O-acyltransferase
38d1fs1b2



not modelled 16.6 33 Fold:POZ domain
Superfamily:POZ domain
Family:BTB/POZ domain
39c2gdvA_



not modelled 16.1 5 PDB header:transferase
Chain: A: PDB Molecule:sucrose phosphorylase;
PDBTitle: sucrose phosphorylase from bifidobacterium adolescentis2 reacted with sucrose
40d1puza_



not modelled 15.7 15 Fold:YgfY-like
Superfamily:YgfY-like
Family:YgfY-like
41d1or7a1



not modelled 15.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
42c2vdcF_



not modelled 15.0 14 PDB header:oxidoreductase
Chain: F: PDB Molecule:glutamate synthase [nadph] large chain;
PDBTitle: the 9.5 a resolution structure of glutamate synthase from2 cryo-electron microscopy and its oligomerization behavior3 in solution: functional implications.
43d1nexa2



not modelled 14.9 33 Fold:POZ domain
Superfamily:POZ domain
Family:BTB/POZ domain
44d2i3oa1



not modelled 14.5 10 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Gamma-glutamyltranspeptidase-like
45c2w31A_



not modelled 13.9 7 PDB header:oxygen transport
Chain: A: PDB Molecule:globin;
PDBTitle: globin domain of geobacter sulfurreducens globin-coupled2 sensor
46c1e6yE_



not modelled 13.9 33 PDB header:oxidoreductase
Chain: E: PDB Molecule:methyl-coenzyme m reductase i beta subunit;
PDBTitle: methyl-coenzyme m reductase from methanosarcina barkeri
47d1xl7a2



not modelled 13.8 21 Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:Choline/Carnitine O-acyltransferase
48d2hc5a1



not modelled 13.8 13 Fold:FlaG-like
Superfamily:FlaG-like
Family:FlaG-like
49c2rnqA_



not modelled 13.6 36 PDB header:transcription
Chain: A: PDB Molecule:transcription initiation factor iie subunit
PDBTitle: solution structure of the c-terminal acidic domain of tfiie2 alpha
50c2jtxA_



not modelled 13.6 36 PDB header:transcription
Chain: A: PDB Molecule:transcription initiation factor iie subunit
PDBTitle: nmr structure of the tfiie-alpha carboxyl terminus
51c1dvpA_



not modelled 13.3 13 PDB header:transferase
Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine
PDBTitle: crystal structure of the vhs and fyve tandem domains of hrs,2 a protein involved in membrane trafficking and signal3 transduction
52c2lcvA_



not modelled 13.1 17 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional repressor cytr;
PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
53d1e6yb1



not modelled 13.1 33 Fold:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
54c3g5bA_



not modelled 13.0 16 PDB header:apoptosis
Chain: A: PDB Molecule:netrin receptor unc5b;
PDBTitle: the structure of unc5b cytoplasmic domain
55c3jroC_



not modelled 13.0 19 PDB header:transport protein, structural protein
Chain: C: PDB Molecule:nucleoporin nup84;
PDBTitle: nup84-nup145c-sec13 edge element of the npc lattice
56c1xrxD_



not modelled 12.9 29 PDB header:replication inhibitor
Chain: D: PDB Molecule:seqa protein;
PDBTitle: crystal structure of a dna-binding protein
57d1xrxa1



not modelled 12.9 29 Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:SeqA N-terminal domain-like
58c3qp5C_



not modelled 12.7 12 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
59d1e6vb1



not modelled 12.6 33 Fold:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
60d1v74b_



not modelled 12.3 25 Fold:Four-helical up-and-down bundle
Superfamily:Colicin D immunity protein
Family:Colicin D immunity protein
61d1hw6a_



not modelled 12.1 15 Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
62d1l3la1



not modelled 12.1 10 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)
63c2krfB_



not modelled 12.0 8 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
64d1fsea_



not modelled 11.9 20 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)
65c3lvzA_



not modelled 11.9 12 PDB header:hydrolase
Chain: A: PDB Molecule:blr6230 protein;
PDBTitle: new refinement of the crystal structure of bjp-1, a subclass b32 metallo-beta-lactamase of bradyrhizobium japonicum
66c3sztB_



not modelled 11.8 13 PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone
67c2jq6A_



not modelled 11.3 17 PDB header:metal binding protein
Chain: A: PDB Molecule:eh domain-containing protein 1;
PDBTitle: structure of eh-domain of ehd1
68d1q5ma_



not modelled 11.3 14 Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
69c2jpcA_



not modelled 11.1 10 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
70c2hpcF_



not modelled 11.1 38 PDB header:blood clotting
Chain: F: PDB Molecule:fibrinogen, gamma polypeptide;
PDBTitle: crystal structure of fragment d from human fibrinogen complexed with2 gly-pro-arg-pro-amide.
71d1gvia3



not modelled 11.0 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
72c3fiaA_



not modelled 10.9 13 PDB header:protein binding
Chain: A: PDB Molecule:intersectin-1;
PDBTitle: crystal structure of the eh 1 domain from human intersectin-2 1 protein. northeast structural genomics consortium target3 hr3646e.
73c1qhoA_



not modelled 10.9 13 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
74d2pbea1



not modelled 10.8 18 Fold:PAP/OAS1 substrate-binding domain
Superfamily:PAP/OAS1 substrate-binding domain
Family:AadK C-terminal domain-like
75c3kblA_



not modelled 10.8 38 PDB header:protein binding
Chain: A: PDB Molecule:female germline-specific tumor suppressor gld-1;
PDBTitle: crystal structure of the gld-1 homodimerization domain from2 caenorhabditis elegans n169a mutant at 2.28 a resolution
76d2ve8a1



not modelled 10.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:FtsK C-terminal domain-like
77c2qy7A_



not modelled 10.6 18 PDB header:protein binding
Chain: A: PDB Molecule:clathrin interactor 1;
PDBTitle: crystal structure of human epsinr enth domain
78d1q7ha2



not modelled 10.6 46 Fold:Cystatin-like
Superfamily:Pre-PUA domain
Family:Hypothetical protein Ta1423, N-terminal domain
79d1tuka1



not modelled 10.6 27 Fold:Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Superfamily:Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
Family:Plant lipid-transfer and hydrophobic proteins
80d1c01a_



not modelled 10.5 27 Fold:gamma-Crystallin-like
Superfamily:gamma-Crystallin-like
Family:Plant antimicrobial protein MIAMP1
81d1nn7a_



not modelled 10.3 14 Fold:POZ domain
Superfamily:POZ domain
Family:Tetramerization domain of potassium channels
82d1j20a2



not modelled 10.3 17 Fold:Argininosuccinate synthetase, C-terminal domain
Superfamily:Argininosuccinate synthetase, C-terminal domain
Family:Argininosuccinate synthetase, C-terminal domain
83d1s1ga_



not modelled 10.3 14 Fold:POZ domain
Superfamily:POZ domain
Family:Tetramerization domain of potassium channels
84d2esha1



not modelled 10.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PadR-like
85c3bvhC_



not modelled 10.2 31 PDB header:blood clotting
Chain: C: PDB Molecule:fibrinogen gamma chain;
PDBTitle: crystal structure of recombinant gammad364a fibrinogen fragment d with2 the peptide ligand gly-pro-arg-pro-amide
86c2kmgA_



not modelled 10.2 26 PDB header:gene regulation
Chain: A: PDB Molecule:klca;
PDBTitle: the structure of the klca and ardb proteins show a novel2 fold and antirestriction activity against type i dna3 restriction systems in vivo but not in vitro
87c2rnjA_



not modelled 10.2 15 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
88d1ofda3



not modelled 10.1 21 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Class II glutamine amidotransferases
89c1nexC_



not modelled 10.0 36 PDB header:ligase, cell cycle
Chain: C: PDB Molecule:centromere dna-binding protein complex cbf3
PDBTitle: crystal structure of scskp1-sccdc4-cpd peptide complex
90c2q0oA_



not modelled 10.0 2 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
91d2c9wc1



not modelled 10.0 36 Fold:POZ domain
Superfamily:POZ domain
Family:BTB/POZ domain
92c1lm1A_



not modelled 9.9 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:ferredoxin-dependent glutamate synthase;
PDBTitle: structural studies on the synchronization of catalytic centers in2 glutamate synthase: native enzyme
93d1ug7a_



not modelled 9.8 16 Fold:Four-helical up-and-down bundle
Superfamily:Domain from hypothetical 2610208m17rik protein
Family:Domain from hypothetical 2610208m17rik protein
94c3k8kB_



not modelled 9.8 21 PDB header:membrane protein
Chain: B: PDB Molecule:alpha-amylase, susg;
PDBTitle: crystal structure of susg
95d1ht6a2



not modelled 9.8 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
96c2cblA_



not modelled 9.8 15 PDB header:complex (proto-oncogene/peptide)
Chain: A: PDB Molecule:proto-oncogene cbl;
PDBTitle: n-terminal domain of cbl in complex with its binding site2 on zap-70
97d1inza_



not modelled 9.8 13 Fold:alpha-alpha superhelix
Superfamily:ENTH/VHS domain
Family:ENTH domain
98d1ea9c3



not modelled 9.8 18 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
99c3excX_



not modelled 9.7 15 PDB header:hydrolase
Chain: X: PDB Molecule:uncharacterized protein;
PDBTitle: structure of the rna'se sso8090 from sulfolobus solfataricus

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