Secondary structure and disorder prediction

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10

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20

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30

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40

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50

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60

Sequence

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K

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C

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L

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A

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A

E

C

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I

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S

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I

D

Y

G

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A

A

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V

D

R

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T

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L

A

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V

M

Q

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

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90

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100

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110

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120

Sequence

C

D

Q

D

A

H

I

R

V

Q

L

N

T

A

N

I

S

N

N

G

F

G

F

G

P

N

G

S

L

N

L

I

A

S

D

A

F

S

G

S

N

N

L

D

L

A

L

A

S

G

K

N

D

N

P

G

S

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G

T

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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140

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150

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160

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170

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180

Sequence

A

S

I

S

T

S

P

N

N

W

L

V

F

M

Q

N

G

Q

E

V

V

I

D

S

G

K

S

V

S

L

T

L

T

M

A

P

A

F

K

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E

G

E

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M

T

D

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N

L

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A

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

K

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

Rank Aligned region

PDB 2w07 chain B Region: 21 - 106 Aligned: 78 Modelled: 86 Confidence: 94.8% Identity: 19% PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf Phyre2 PDB 3bfw chain A Region: 18 - 125 Aligned: 104 Modelled: 108 Confidence: 94.7% Identity: 15% PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf) Phyre2 PDB 3jwn chain K Region: 21 - 106 Aligned: 81 Modelled: 86 Confidence: 94.1% Identity: 17% PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 1klf chain P Region: 21 - 106 Aligned: 69 Modelled: 72 Confidence: 93.9% Identity: 13% PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose Phyre2 PDB 3jwn chain E Region: 21 - 126 Aligned: 101 Modelled: 106 Confidence: 93.8% Identity: 16% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 1ze3 chain H domain 1 Region: 21 - 106 Aligned: 69 Modelled: 69 Confidence: 93.3% Identity: 12% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3jwn chain L Region: 21 - 126 Aligned: 103 Modelled: 106 Confidence: 93.3% Identity: 17% PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain F Region: 21 - 126 Aligned: 103 Modelled: 106 Confidence: 92.9% Identity: 17% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 1n12 chain A Region: 21 - 155 Aligned: 123 Modelled: 135 Confidence: 87.9% Identity: 14% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2jty chain A Region: 21 - 125 Aligned: 100 Modelled: 105 Confidence: 77.9% Identity: 14% PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus Phyre2 PDB 2uy6 chain B domain 1 Region: 21 - 125 Aligned: 101 Modelled: 101 Confidence: 70.7% Identity: 13% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2j2z chain B domain 1 Region: 21 - 123 Aligned: 97 Modelled: 97 Confidence: 65.5% Identity: 15% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1pdk chain B Region: 18 - 88 Aligned: 68 Modelled: 71 Confidence: 60.7% Identity: 9% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2wmp chain B Region: 19 - 78 Aligned: 52 Modelled: 60 Confidence: 47.1% Identity: 25% PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin Phyre2 PDB 2vsv chain B Region: 63 - 147 Aligned: 58 Modelled: 85 Confidence: 41.4% Identity: 14% PDB header:protein-binding Chain: B: PDB Molecule:rhophilin-2; PDBTitle: crystal structure of the pdz domain of human rhophilin-2 Phyre2 PDB 3qbt chain H Region: 22 - 69 Aligned: 38 Modelled: 48 Confidence: 34.1% Identity: 11% PDB header:protein transport/hydrolase Chain: H: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1; PDBTitle: crystal structure of ocrl1 540-678 in complex with rab8a:gppnhp Phyre2 PDB 1r6j chain A Region: 63 - 158 Aligned: 67 Modelled: 81 Confidence: 29.6% Identity: 28% Fold: PDZ domain-like Superfamily: PDZ domain-like Family: PDZ domain Phyre2 PDB 1r6j chain A Region: 63 - 158 Aligned: 67 Modelled: 81 Confidence: 29.6% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:syntenin 1; PDBTitle: ultrahigh resolution crystal structure of syntenin pdz2 Phyre2 PDB 1nte chain A Region: 63 - 158 Aligned: 67 Modelled: 81 Confidence: 29.6% Identity: 28% PDB header:signaling protein Chain: A: PDB Molecule:syntenin 1; PDBTitle: crystal structure analysis of the second pdz domain of2 syntenin Phyre2 PDB 3khf chain A Region: 78 - 164 Aligned: 76 Modelled: 87 Confidence: 21.2% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:microtubule-associated serine/threonine-protein PDBTitle: the crystal structure of the pdz domain of human microtubule2 associated serine/threonine kinase 3 (mast3) Phyre2 1 c2w07B_ 2 c3bfwA_ 3 c3jwnK_ 4 c1klfP_ 5 c3jwnE_ 6 d1ze3h1 7 c3jwnL_ 8 c3jwnF_ 9 d1n12a_ 10 c2jtyA_ 11 d2uy6b1 12 d2j2zb1 13 d1pdkb_ 14 c2wmpB_ 15 c2vsvB_ 16 c3qbtH_ 17 d1r6ja_ 18 c1r6jA_ 19 c1nteA_ 20 c3khfA_ 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

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2w07B_ 94.8 19 PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf 2 c3bfwA_ 94.7 15 PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf) 3 c3jwnK_ 94.1 17 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c1klfP_ 93.9 13 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 5 c3jwnE_ 93.8 16 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 6 d1ze3h1 93.3 12 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 7 c3jwnL_ 93.3 17 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 8 c3jwnF_ 92.9 17 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 9 d1n12a_ 87.9 14 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 10 c2jtyA_ 77.9 14 PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus 11 d2uy6b1 70.7 13 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 12 d2j2zb1 65.5 15 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 13 d1pdkb_ 60.7 9 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 14 c2wmpB_ 47.1 25 PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin 15 c2vsvB_ 41.4 14 PDB header:protein-binding Chain: B: PDB Molecule:rhophilin-2; PDBTitle: crystal structure of the pdz domain of human rhophilin-2 16 c3qbtH_ 34.1 11 PDB header:protein transport/hydrolase Chain: H: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1; PDBTitle: crystal structure of ocrl1 540-678 in complex with rab8a:gppnhp 17 d1r6ja_ 29.6 28 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 18 c1r6jA_ 29.6 28 PDB header:membrane protein Chain: A: PDB Molecule:syntenin 1; PDBTitle: ultrahigh resolution crystal structure of syntenin pdz2 19 c1nteA_ 29.6 28 PDB header:signaling protein Chain: A: PDB Molecule:syntenin 1; PDBTitle: crystal structure analysis of the second pdz domain of2 syntenin 20 c3khfA_ 21.2 16 PDB header:transferase Chain: A: PDB Molecule:microtubule-associated serine/threonine-protein PDBTitle: the crystal structure of the pdz domain of human microtubule2 associated serine/threonine kinase 3 (mast3) 21 c2kjmA_ not modelled 18.4 50 PDB header:rna binding protein Chain: A: PDB Molecule:histone rna hairpin-binding protein; PDBTitle: solution structure of slbp rna binding domain fragment 22 c3qglD_ not modelled 17.8 16 PDB header:protein binding Chain: D: PDB Molecule:sorting nexin-27; PDBTitle: crystal structure of pdz domain of sorting nexin 27 (snx27) in complex2 with the eseskv peptide corresponding to the c-terminal tail of girk3 23 d1eaqa_ not modelled 16.5 55 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:RUNT domain 24 d1ljma_ not modelled 16.0 55 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:RUNT domain 25 c1y7nA_ not modelled 15.9 22 PDB header:protein transport Chain: A: PDB Molecule:amyloid beta a4 precursor protein-binding family PDBTitle: solution structure of the second pdz domain of the human2 neuronal adaptor x11alpha 26 d1ry4a_ not modelled 11.8 20 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 27 c3l4fD_ not modelled 10.9 18 PDB header:signaling protein/protein binding Chain: D: PDB Molecule:sh3 and multiple ankyrin repeat domains protein PDBTitle: crystal structure of betapix coiled-coil domain and shank2 pdz complex 28 d1auua_ not modelled 10.6 25 Fold:GroES-like Superfamily:SacY-like RNA-binding domain Family:BglG-like antiterminator proteins 29 c1u39A_ not modelled 10.2 16 PDB header:protein transport Chain: A: PDB Molecule:amyloid beta a4 precursor protein-binding, PDBTitle: auto-inhibition mechanism of x11s/mints family scaffold2 proteins revealed by the closed conformation of the tandem3 pdz domains 30 d1hcza1 not modelled 10.1 20 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 31 d2oz4a1 not modelled 9.9 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C2 set domains 32 c2jtvA_ not modelled 9.9 22 PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 33 d1uf1a_ not modelled 9.8 12 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 34 c7mdhA_ not modelled 9.3 10 PDB header:chloroplastic malate dehydrogenase Chain: A: PDB Molecule:protein (malate dehydrogenase); PDBTitle: structural basis for light acitvation of a chloroplast enzyme. the2 structure of sorghum nadp-malate dehydrogenase in its oxidized form 35 c2eaqA_ not modelled 9.3 13 PDB header:metal binding protein Chain: A: PDB Molecule:lim domain only protein 7; PDBTitle: crystal structure of pdz domain of kiaa0858 (lim), ms07932 from homo sapiens 36 d1b8pa2 not modelled 9.0 10 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 37 c2yzyA_ not modelled 8.9 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative uncharacterized protein ttha1012; PDBTitle: crystal structure of uncharacterized conserved protein from thermus2 thermophilus hb8 38 d1kwaa_ not modelled 8.5 21 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 39 d1yq2a3 not modelled 8.3 29 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:beta-Galactosidase/glucuronidase, N-terminal domain 40 d1y7na1 not modelled 8.1 21 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 41 c2k8pA_ not modelled 8.0 18 PDB header:signaling protein Chain: A: PDB Molecule:sclerostin; PDBTitle: characterisation of the structural features and2 interactions of sclerostin: molecular insight into a key3 regulator of wnt-mediated bone formation 42 d7mdha2 not modelled 8.0 10 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 43 d1wioa2 not modelled 7.4 43 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 44 c2z17A_ not modelled 7.3 17 PDB header:protein binding Chain: A: PDB Molecule:pleckstrin homology sec7 and coiled-coil domains- PDBTitle: crystal sturcture of pdz domain from human pleckstrin2 homology, sec7 45 d1civa2 not modelled 7.3 9 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 46 d1jz8a3 not modelled 7.3 11 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:beta-Galactosidase/glucuronidase, N-terminal domain 47 c2d8iA_ not modelled 7.2 16 PDB header:immune system, signaling protein Chain: A: PDB Molecule:t-cell lymphoma invasion and metastasis 1 PDBTitle: solution structure of the pdz domain of t-cell lymphoma2 invasion and metastasis 1 varian 48 c2w95B_ not modelled 7.1 12 PDB header:cell adhesion Chain: B: PDB Molecule:discoidin-1 subunit a; PDBTitle: structure of the discoidin i from dictyostelium discoideum2 in complex with galnac at 1.75 angstrom resolution 49 c2fc6A_ not modelled 6.9 27 PDB header:transcription Chain: A: PDB Molecule:target of egr1, member 1; PDBTitle: solution structure of the zf-ccch domain of target of egr1,2 member 1 (nuclear) 50 c2jmrA_ not modelled 6.8 13 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 51 d2fc6a1 not modelled 6.4 44 Fold:CCCH zinc finger Superfamily:CCCH zinc finger Family:CCCH zinc finger 52 c2kv8A_ not modelled 6.3 19 PDB header:signaling protein Chain: A: PDB Molecule:regulator of g-protein signaling 12; PDBTitle: solution structure ofrgs12 pdz domain 53 d1gv0a2 not modelled 6.2 8 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 54 c1wziA_ not modelled 6.1 14 PDB header:oxidoreductase Chain: A: PDB Molecule:malate dehydrogenase; PDBTitle: structural basis for alteration of cofactor specificity of2 malate dehydrogenase from thermus flavus 55 d1be9a_ not modelled 6.0 13 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 56 d1y7ta2 not modelled 5.9 14 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 57 d2zjrp1 not modelled 5.7 15 Fold:Ribosomal protein L22 Superfamily:Ribosomal protein L22 Family:Ribosomal protein L22 58 c2xzzA_ not modelled 5.6 10 PDB header:transferase Chain: A: PDB Molecule:protein-glutamine gamma-glutamyltransferase k; PDBTitle: crystal structure of the human transglutaminase 1 beta-barrel domain 59 c2nncB_ not modelled 5.4 10 PDB header:ligand binding protein Chain: B: PDB Molecule:sulfur covalently-binding protein; PDBTitle: structure of the sulfur carrier protein soxy from chlorobium limicola2 f thiosulfatophilum 60 c1b8vA_ not modelled 5.3 12 PDB header:oxidoreductase Chain: A: PDB Molecule:protein (malate dehydrogenase); PDBTitle: malate dehydrogenase from aquaspirillum arcticum 61 d1hyha2 not modelled 5.1 15 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 62 c1xt5A_ not modelled 5.1 4 PDB header:immune system Chain: A: PDB Molecule:variable region-containing chitin-binding PDBTitle: crystal structure of vcbp3, domain 1, from branchiostoma2 floridae

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