Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP75711
DateThu Jan 5 12:13:19 GMT 2012
Unique Job ID64c8785847c8e774

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2k4jA_
Top template information
PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: arsr dna binding domain
Confidence and coverage
Confidence: 48.2% Coverage: 68%
63 residues ( 68% of your sequence) have been modelled with 48.2% 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  MNRPAILKKKAAKDVASVLKIIFLFYLFLIARLKQRYSIREIKRDLWNIRENYSSNAAIA
Secondary structure 

SS confidence 



























































Disorder  ????


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Disorder confidence 



























































 
   .........70.........80.........90..
Sequence  KIYCRKRKASGPGKHLTILPYGWVRFITFPIM
Secondary structure 












SS confidence 































Disorder 



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????
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 2k4j chain A

3D model

Region: 23 - 85
Aligned: 63
Modelled: 63
Confidence: 48.2%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: arsr dna binding domain

Phyre2

PDB 1opc chain A

3D model

Region: 23 - 85
Aligned: 63
Modelled: 63
Confidence: 35.8%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2

PDB 2v1y chain A

3D model

Region: 38 - 54
Aligned: 17
Modelled: 17
Confidence: 33.6%
Identity: 24%
PDB header:transferase
Chain: A: PDB Molecule:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic
PDBTitle: structure of a phosphoinositide 3-kinase alpha adaptor-2 binding domain (abd) in a complex with the ish2 domain3 from p85 alpha

Phyre2

PDB 1gxq chain A

3D model

Region: 23 - 85
Aligned: 63
Modelled: 63
Confidence: 31.1%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: PhoB-like

Phyre2

PDB 3q9v chain B

3D model

Region: 23 - 85
Aligned: 63
Modelled: 63
Confidence: 31.1%
Identity: 25%
PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra c-terminal domain(123-221) from deinococcus2 radiodurans

Phyre2

PDB 2hqn chain A

3D model

Region: 23 - 85
Aligned: 63
Modelled: 63
Confidence: 29.5%
Identity: 19%
PDB header:signaling protein
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism

Phyre2

PDB 2hwv chain A

3D model

Region: 23 - 75
Aligned: 53
Modelled: 53
Confidence: 27.1%
Identity: 11%
PDB header:transcription
Chain: A: PDB Molecule:dna-binding response regulator vicr;
PDBTitle: crystal structure of an essential response regulator dna binding2 domain, vicrc in enterococcus faecalis, a member of the yycf3 subfamily.

Phyre2

PDB 2kq0 chain A

3D model

Region: 78 - 88
Aligned: 11
Modelled: 11
Confidence: 25.2%
Identity: 36%
PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase nedd4;
PDBTitle: human nedd4 3rd ww domain complex with ebola zaire virus matrix2 protein vp40 derived peptide ilptappeymea

Phyre2

PDB 2vxz chain A

3D model

Region: 39 - 53
Aligned: 15
Modelled: 15
Confidence: 14.9%
Identity: 7%
PDB header:viral protein
Chain: A: PDB Molecule:pyrsv_gp04;
PDBTitle: crystal structure of hypothetical protein pyrsv_gp04 from2 pyrobaculum spherical virus

Phyre2

PDB 3q9s chain A

3D model

Region: 23 - 75
Aligned: 53
Modelled: 53
Confidence: 13.2%
Identity: 23%
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra(1-215) from deinococcus radiodurans

Phyre2

PDB 2j7u chain A

3D model

Region: 24 - 88
Aligned: 65
Modelled: 65
Confidence: 12.7%
Identity: 28%
PDB header:viral protein
Chain: A: PDB Molecule:rna dependent rna polymerase;
PDBTitle: dengue virus ns5 rna dependent rna polymerase domain

Phyre2

PDB 2f21 chain A domain 1

3D model

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 12.7%
Identity: 40%
Fold: WW domain-like
Superfamily: WW domain
Family: WW domain

Phyre2

PDB 2kyk chain A

3D model

Region: 73 - 88
Aligned: 16
Modelled: 16
Confidence: 11.4%
Identity: 38%
PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase itchy homolog;
PDBTitle: the sandwich region between two lmp2a py motif regulates the2 interaction between aip4ww2domain and py motif

Phyre2

PDB 2zxj chain B

3D model

Region: 20 - 85
Aligned: 66
Modelled: 66
Confidence: 10.4%
Identity: 12%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein walr;
PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus

Phyre2

PDB 2laz chain A

3D model

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 10.1%
Identity: 40%
PDB header:signaling protein/transcription
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase smurf1;
PDBTitle: structure of the first ww domain of human smurf1 in complex with a2 mono-phosphorylated human smad1 derived peptide

Phyre2

PDB 1wmv chain A

3D model

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 9.9%
Identity: 50%
PDB header:oxidoreductase, apoptosis
Chain: A: PDB Molecule:ww domain containing oxidoreductase;
PDBTitle: solution structure of the second ww domain of wwox

Phyre2

PDB 3ml6 chain D

3D model

Region: 80 - 88
Aligned: 9
Modelled: 9
Confidence: 9.8%
Identity: 44%
PDB header:protein transport
Chain: D: PDB Molecule:chimeric complex between protein dishevlled2 homolog dvl-2
PDBTitle: a complex between dishevlled2 and clathrin adaptor ap-2

Phyre2

PDB 2jzy chain A

3D model

Region: 23 - 78
Aligned: 56
Modelled: 56
Confidence: 9.7%
Identity: 14%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein pcor;
PDBTitle: solution structure of c-terminal effector domain of2 putative two-component-system response regulator involved3 in copper resistance from klebsiella pneumoniae

Phyre2

PDB 2zaj chain A

3D model

Region: 79 - 88
Aligned: 10
Modelled: 10
Confidence: 9.7%
Identity: 40%
PDB header:protein binding
Chain: A: PDB Molecule:membrane-associated guanylate kinase, ww and pdz
PDBTitle: solution structure of the short-isoform of the second ww2 domain from the human membrane-associated guanylate kinase,3 ww and pdz domain-containing protein 1 (magi-1)

Phyre2

PDB 1k6n chain H

3D model

Region: 14 - 44
Aligned: 27
Modelled: 31
Confidence: 9.6%
Identity: 37%
PDB header:photosynthesis
Chain: H: PDB Molecule:photosynthetic reaction center h subunit;
PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides

Phyre2
1

c2k4jA_
2

d1opca_
3

c2v1yA_
4

d1gxqa_
5

c3q9vB_
6

c2hqnA_
7

c2hwvA_
8

c2kq0A_
9

c2vxzA_
10

c3q9sA_
11

c2j7uA_
12

d2f21a1
13

c2kykA_
14

c2zxjB_
15

c2lazA_
16

c1wmvA_
17

c3ml6D_
18

c2jzyA_
19

c2zajA_
20

c1k6nH_
21



22



23



24



25



26



27



28



29



30



31



32



33



34



35



36



37



38



39



40



41



42



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44



45



46



47



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49



50



51



52



53



54



55



56



57



58



59



60



61



62






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2k4jA_



48.2 16 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: arsr dna binding domain
2d1opca_



35.8 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:PhoB-like
3c2v1yA_



33.6 24 PDB header:transferase
Chain: A: PDB Molecule:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic
PDBTitle: structure of a phosphoinositide 3-kinase alpha adaptor-2 binding domain (abd) in a complex with the ish2 domain3 from p85 alpha
4d1gxqa_



31.1 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:PhoB-like
5c3q9vB_



31.1 25 PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra c-terminal domain(123-221) from deinococcus2 radiodurans
6c2hqnA_



29.5 19 PDB header:signaling protein
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism
7c2hwvA_



27.1 11 PDB header:transcription
Chain: A: PDB Molecule:dna-binding response regulator vicr;
PDBTitle: crystal structure of an essential response regulator dna binding2 domain, vicrc in enterococcus faecalis, a member of the yycf3 subfamily.
8c2kq0A_



25.2 36 PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase nedd4;
PDBTitle: human nedd4 3rd ww domain complex with ebola zaire virus matrix2 protein vp40 derived peptide ilptappeymea
9c2vxzA_



14.9 7 PDB header:viral protein
Chain: A: PDB Molecule:pyrsv_gp04;
PDBTitle: crystal structure of hypothetical protein pyrsv_gp04 from2 pyrobaculum spherical virus
10c3q9sA_



13.2 23 PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra(1-215) from deinococcus radiodurans
11c2j7uA_



12.7 28 PDB header:viral protein
Chain: A: PDB Molecule:rna dependent rna polymerase;
PDBTitle: dengue virus ns5 rna dependent rna polymerase domain
12d2f21a1



12.7 40 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
13c2kykA_



11.4 38 PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase itchy homolog;
PDBTitle: the sandwich region between two lmp2a py motif regulates the2 interaction between aip4ww2domain and py motif
14c2zxjB_



10.4 12 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein walr;
PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus
15c2lazA_



10.1 40 PDB header:signaling protein/transcription
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase smurf1;
PDBTitle: structure of the first ww domain of human smurf1 in complex with a2 mono-phosphorylated human smad1 derived peptide
16c1wmvA_



9.9 50 PDB header:oxidoreductase, apoptosis
Chain: A: PDB Molecule:ww domain containing oxidoreductase;
PDBTitle: solution structure of the second ww domain of wwox
17c3ml6D_



9.8 44 PDB header:protein transport
Chain: D: PDB Molecule:chimeric complex between protein dishevlled2 homolog dvl-2
PDBTitle: a complex between dishevlled2 and clathrin adaptor ap-2
18c2jzyA_



9.7 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein pcor;
PDBTitle: solution structure of c-terminal effector domain of2 putative two-component-system response regulator involved3 in copper resistance from klebsiella pneumoniae
19c2zajA_



9.7 40 PDB header:protein binding
Chain: A: PDB Molecule:membrane-associated guanylate kinase, ww and pdz
PDBTitle: solution structure of the short-isoform of the second ww2 domain from the human membrane-associated guanylate kinase,3 ww and pdz domain-containing protein 1 (magi-1)
20c1k6nH_



9.6 37 PDB header:photosynthesis
Chain: H: PDB Molecule:photosynthetic reaction center h subunit;
PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides
21c2lb0A_



not modelled 9.0 40 PDB header:signaling protein/transcription
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase smurf1;
PDBTitle: structure of the first ww domain of human smurf1 in complex with a di-2 phosphorylated human smad1 derived peptide
22c2pmuD_



not modelled 8.9 18 PDB header:transcription regulation
Chain: D: PDB Molecule:response regulator phop;
PDBTitle: crystal structure of the dna-binding domain of phop
23d1tk7a2



not modelled 8.8 50 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
24c2dmvA_



not modelled 8.8 40 PDB header:ligase
Chain: A: PDB Molecule:itchy homolog e3 ubiquitin protein ligase;
PDBTitle: solution structure of the second ww domain of itchy homolog2 e3 ubiquitin protein ligase (itch)
25c3l81A_



not modelled 8.7 44 PDB header:transport protein
Chain: A: PDB Molecule:ap-4 complex subunit mu-1;
PDBTitle: crystal structure of adaptor protein complex 4 (ap-4) mu4 subunit c-2 terminal domain, in complex with a sorting peptide from the amyloid3 precursor protein (app)
26d1wfxa_



not modelled 8.4 18 Fold:ADP-ribosylation
Superfamily:ADP-ribosylation
Family:Tpt1/KptA
27c2ysbA_



not modelled 8.3 50 PDB header:protein binding
Chain: A: PDB Molecule:salvador homolog 1 protein;
PDBTitle: solution structure of the first ww domain from the mouse2 salvador homolog 1 protein (sav1)
28c1bw8A_



not modelled 8.3 44 PDB header:peptide binding protein
Chain: A: PDB Molecule:protein (mu2 adaptin subunit);
PDBTitle: mu2 adaptin subunit (ap50) of ap2 adaptor (second domain),2 complexed with egfr internalization peptide fyralm
29c2lawA_



not modelled 8.0 50 PDB header:signaling protein/transcription
Chain: A: PDB Molecule:yorkie homolog;
PDBTitle: structure of the second ww domain from human yap in complex with a2 human smad1 derived peptide
30c1eysH_



not modelled 7.9 41 PDB header:electron transport
Chain: H: PDB Molecule:photosynthetic reaction center;
PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum
31d1i8gb_



not modelled 7.8 40 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
32c2jmfA_



not modelled 7.7 50 PDB header:ligase/signaling protein
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase suppressor of deltex;
PDBTitle: solution structure of the su(dx) ww4- notch py peptide2 complex
33d2pr9a1



not modelled 7.6 44 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
Family:Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
34c1ymzA_



not modelled 7.5 50 PDB header:unknown function
Chain: A: PDB Molecule:cc45;
PDBTitle: cc45, an artificial ww domain designed using statistical2 coupling analysis
35c1wr7A_



not modelled 7.3 50 PDB header:ligase
Chain: A: PDB Molecule:nedd4-2;
PDBTitle: solution structure of the third ww domain of nedd4-2
36c2l4jA_



not modelled 7.2 60 PDB header:transcription
Chain: A: PDB Molecule:yes-associated protein 2 (yap2);
PDBTitle: yap ww2
37c2yshA_



not modelled 7.2 40 PDB header:protein binding
Chain: A: PDB Molecule:growth-arrest-specific protein 7;
PDBTitle: solution structure of the ww domain from the human growth-2 arrest-specific protein 7, gas-7
38d1ys7a1



not modelled 7.2 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:PhoB-like
39c2gwwB_



not modelled 7.1 50 PDB header:cell adhesion, structural protein
Chain: B: PDB Molecule:ipaa;
PDBTitle: human vinculin (head domain, vh1, residues 1-258) in2 complex with shigella's ipaa vinculin binding site3 (residues 602-633)
40c3ll6B_



not modelled 7.1 30 PDB header:transferase
Chain: B: PDB Molecule:cyclin g-associated kinase;
PDBTitle: crystal structure of the human cyclin g associated kinase (gak)
41d1nmva1



not modelled 7.0 40 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
42d2jmfa1



not modelled 6.8 50 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
43d1f8ab1



not modelled 6.7 40 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
44c1wr4A_



not modelled 6.7 40 PDB header:ligase
Chain: A: PDB Molecule:ubiquitin-protein ligase nedd4-2;
PDBTitle: solution structure of the second ww domain of nedd4-2
45c3ogfA_



not modelled 6.6 43 PDB header:de novo protein
Chain: A: PDB Molecule:de novo designed dimeric trefoil-fold sub-domain which
PDBTitle: crystal structure of difoil-4p homo-trimer: de novo designed dimeric2 trefoil-fold sub-domain which forms homo-trimer assembly
46c1e0mA_



not modelled 6.5 50 PDB header:de novo protein
Chain: A: PDB Molecule:wwprototype;
PDBTitle: prototype ww domain
47c2ez5W_



not modelled 6.5 30 PDB header:signalling protein,ligase
Chain: W: PDB Molecule:e3 ubiquitin-protein ligase nedd4;
PDBTitle: solution structure of the dnedd4 ww3* domain- comm lpsy2 peptide complex
48c1w63P_



not modelled 6.3 56 PDB header:endocytosis
Chain: P: PDB Molecule:adaptor-related protein complex 1, mu 1 subunit;
PDBTitle: ap1 clathrin adaptor core
49d1tk7a1



not modelled 6.2 50 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
50c1yiuA_



not modelled 6.2 40 PDB header:ligase
Chain: A: PDB Molecule:itchy e3 ubiquitin protein ligase;
PDBTitle: itch e3 ubiquitin ligase ww3 domain
51c2oqrA_



not modelled 6.2 8 PDB header:transcription,signaling protein
Chain: A: PDB Molecule:sensory transduction protein regx3;
PDBTitle: the structure of the response regulator regx3 from mycobacterium2 tuberculosis
52d1iqoa_



not modelled 6.0 21 Fold:Hypothetical protein MTH1880
Superfamily:Hypothetical protein MTH1880
Family:Hypothetical protein MTH1880
53c2dwvB_



not modelled 5.9 50 PDB header:protein binding
Chain: B: PDB Molecule:salvador homolog 1 protein;
PDBTitle: solution structure of the second ww domain from mouse2 salvador homolog 1 protein (mww45)
54d1k9ra_



not modelled 5.9 50 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
55c2ysgA_



not modelled 5.7 60 PDB header:protein binding
Chain: A: PDB Molecule:syntaxin-binding protein 4;
PDBTitle: solution structure of the ww domain from the human syntaxin-2 binding protein 4
56d1flca2



not modelled 5.7 57 Fold:Flavodoxin-like
Superfamily:SGNH hydrolase
Family:Esterase domain of haemagglutinin-esterase-fusion glycoprotein HEF1
57c2ysdA_



not modelled 5.7 33 PDB header:protein binding
Chain: A: PDB Molecule:membrane-associated guanylate kinase, ww and pdz
PDBTitle: solution structure of the first ww domain from the human2 membrane-associated guanylate kinase, ww and pdz domain-3 containing protein 1. magi-1
58c2ysfA_



not modelled 5.4 50 PDB header:protein binding
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase itchy homolog;
PDBTitle: solution structure of the fourth ww domain from the human2 e3 ubiquitin-protein ligase itchy homolog, itch
59c3ol0C_



not modelled 5.3 46 PDB header:de novo protein
Chain: C: PDB Molecule:de novo designed monomer trefoil-fold sub-domain which
PDBTitle: crystal structure of monofoil-4p homo-trimer: de novo designed monomer2 trefoil-fold sub-domain which forms homo-trimer assembly
60d2csba2



not modelled 5.3 36 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Topoisomerase V repeat domain
61c2jkrM_



not modelled 5.2 44 PDB header:endocytosis
Chain: M: PDB Molecule:ap-2 complex subunit mu-1;
PDBTitle: ap2 clathrin adaptor core with dileucine peptide rm(2 phosphos)qikrllse
62c2ftcK_



not modelled 5.2 0 PDB header:ribosome
Chain: K: PDB Molecule:39s ribosomal protein l19, mitochondrial;
PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome

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