Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	S	L	K	N	Q	Q	G	F	S	L	P	E	V	M	L	A	M	V	L	M	V	M	I	V	T	A	L	S	G	F	Q	R	T	L	M	N	S	L	A	S	R	N	Q	Y	Q	Q	L	W	R	H	G	W	Q	Q	T	Q	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?																																																	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.
Sequence		R	A	I	S	P	P	A	N	W	Q	V	N	R	M	Q	T	S	Q	A	G	C	V	S	I	S	V	T	L	V	S	P	G	G	R	E	G	E	M	T	R	L	H	C	P	N	R	Q
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 3sok chain B Region: 11 - 56 Aligned: 42 Modelled: 46 Confidence: 95.6% Identity: 24% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 1oqw chain A Region: 11 - 59 Aligned: 49 Modelled: 49 Confidence: 94.5% Identity: 8% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2pil chain A Region: 12 - 56 Aligned: 41 Modelled: 45 Confidence: 91.6% Identity: 17% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2ky8 chain A Region: 63 - 97 Aligned: 35 Modelled: 35 Confidence: 62.2% Identity: 17% PDB header:transcription/dna Chain: A: PDB Molecule:methyl-cpg-binding domain protein 2; PDBTitle: solution structure and dynamic analysis of chicken mbd2 methyl binding2 domain bound to a target methylated dna sequence Phyre2 PDB 1ig4 chain A Region: 63 - 96 Aligned: 34 Modelled: 34 Confidence: 55.0% Identity: 12% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: Methyl-CpG-binding domain, MBD Phyre2 PDB 1qk9 chain A Region: 63 - 96 Aligned: 34 Modelled: 34 Confidence: 44.7% Identity: 21% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: Methyl-CpG-binding domain, MBD Phyre2 PDB 1ub1 chain A Region: 63 - 96 Aligned: 34 Modelled: 34 Confidence: 34.0% Identity: 21% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: Methyl-CpG-binding domain, MBD Phyre2 PDB 1w8o chain A domain 1 Region: 63 - 97 Aligned: 35 Modelled: 35 Confidence: 28.3% Identity: 23% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: E-set domains of sugar-utilizing enzymes Phyre2 PDB 3ci0 chain I domain 1 Region: 33 - 101 Aligned: 67 Modelled: 69 Confidence: 25.6% Identity: 7% Fold: Pili subunits Superfamily: Pili subunits Family: GSPII I/J protein-like Phyre2 PDB 2ret chain A domain 1 Region: 30 - 101 Aligned: 71 Modelled: 72 Confidence: 18.9% Identity: 10% Fold: Pili subunits Superfamily: Pili subunits Family: GSPII I/J protein-like Phyre2 PDB 1yfu chain A domain 1 Region: 73 - 105 Aligned: 32 Modelled: 33 Confidence: 15.7% Identity: 19% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 PDB 2jv4 chain A Region: 63 - 106 Aligned: 35 Modelled: 44 Confidence: 13.4% Identity: 20% PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis/trans isomerase; PDBTitle: structure characterisation of pina ww domain and comparison2 with other group iv ww domains, pin1 and ess1 Phyre2 PDB 2uuy chain B domain 1 Region: 95 - 105 Aligned: 11 Modelled: 11 Confidence: 11.4% Identity: 27% Fold: BPTI-like Superfamily: BPTI-like Family: Tick tryptase inhibitor-like Phyre2 PDB 1ymz chain A Region: 63 - 78 Aligned: 16 Modelled: 16 Confidence: 10.2% Identity: 13% PDB header:unknown function Chain: A: PDB Molecule:cc45; PDBTitle: cc45, an artificial ww domain designed using statistical2 coupling analysis Phyre2 PDB 3nct chain C Region: 28 - 93 Aligned: 66 Modelled: 66 Confidence: 9.7% Identity: 20% PDB header:dna binding protein, chaperone Chain: C: PDB Molecule:protein psib; PDBTitle: x-ray crystal structure of the bacterial conjugation factor psib, a2 negative regulator of reca Phyre2 PDB 1e0m chain A Region: 63 - 76 Aligned: 14 Modelled: 14 Confidence: 9.7% Identity: 14% PDB header:de novo protein Chain: A: PDB Molecule:wwprototype; PDBTitle: prototype ww domain Phyre2 PDB 1wr4 chain A Region: 62 - 76 Aligned: 15 Modelled: 15 Confidence: 9.7% Identity: 13% PDB header:ligase Chain: A: PDB Molecule:ubiquitin-protein ligase nedd4-2; PDBTitle: solution structure of the second ww domain of nedd4-2 Phyre2 PDB 1dva chain Y Region: 100 - 103 Aligned: 4 Modelled: 4 Confidence: 9.3% Identity: 50% PDB header:hydrolase/hydrolase inhibitor Chain: Y: PDB Molecule:peptide e-76; PDBTitle: crystal structure of the complex between the peptide exosite inhibitor2 e-76 and coagulation factor viia Phyre2 PDB 1dva chain X Region: 100 - 103 Aligned: 4 Modelled: 4 Confidence: 9.3% Identity: 50% PDB header:hydrolase/hydrolase inhibitor Chain: X: PDB Molecule:peptide e-76; PDBTitle: crystal structure of the complex between the peptide exosite inhibitor2 e-76 and coagulation factor viia Phyre2 PDB 2ret chain E Region: 30 - 95 Aligned: 60 Modelled: 66 Confidence: 8.9% Identity: 15% PDB header:protein transport Chain: E: PDB Molecule:pseudopilin epsi; PDBTitle: the crystal structure of a binary complex of two pseudopilins: epsi2 and epsj from the type 2 secretion system of vibrio vulnificus Phyre2 1 c3sokB_ 2 d1oqwa_ 3 d2pila_ 4 c2ky8A_ 5 d1ig4a_ 6 d1qk9a_ 7 d1ub1a_ 8 d1w8oa1 9 d3ci0i1 10 d2reta1 11 d1yfua1 12 c2jv4A_ 13 d2uuyb1 14 c1ymzA_ 15 c3nctC_ 16 c1e0mA_ 17 c1wr4A_ 18 c1dvaY_ 19 c1dvaX_ 20 c2retE_ 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

Detailed template information

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

1 c3sokB_ 95.6 24 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 2 d1oqwa_ 94.5 8 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 3 d2pila_ 91.6 17 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 4 c2ky8A_ 62.2 17 PDB header:transcription/dna Chain: A: PDB Molecule:methyl-cpg-binding domain protein 2; PDBTitle: solution structure and dynamic analysis of chicken mbd2 methyl binding2 domain bound to a target methylated dna sequence 5 d1ig4a_ 55.0 12 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:Methyl-CpG-binding domain, MBD 6 d1qk9a_ 44.7 21 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:Methyl-CpG-binding domain, MBD 7 d1ub1a_ 34.0 21 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:Methyl-CpG-binding domain, MBD 8 d1w8oa1 28.3 23 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes 9 d3ci0i1 25.6 7 Fold:Pili subunits Superfamily:Pili subunits Family:GSPII I/J protein-like 10 d2reta1 18.9 10 Fold:Pili subunits Superfamily:Pili subunits Family:GSPII I/J protein-like 11 d1yfua1 15.7 19 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 12 c2jv4A_ 13.4 20 PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis/trans isomerase; PDBTitle: structure characterisation of pina ww domain and comparison2 with other group iv ww domains, pin1 and ess1 13 d2uuyb1 11.4 27 Fold:BPTI-like Superfamily:BPTI-like Family:Tick tryptase inhibitor-like 14 c1ymzA_ 10.2 13 PDB header:unknown function Chain: A: PDB Molecule:cc45; PDBTitle: cc45, an artificial ww domain designed using statistical2 coupling analysis 15 c3nctC_ 9.7 20 PDB header:dna binding protein, chaperone Chain: C: PDB Molecule:protein psib; PDBTitle: x-ray crystal structure of the bacterial conjugation factor psib, a2 negative regulator of reca 16 c1e0mA_ 9.7 14 PDB header:de novo protein Chain: A: PDB Molecule:wwprototype; PDBTitle: prototype ww domain 17 c1wr4A_ 9.7 13 PDB header:ligase Chain: A: PDB Molecule:ubiquitin-protein ligase nedd4-2; PDBTitle: solution structure of the second ww domain of nedd4-2 18 c1dvaY_ 9.3 50 PDB header:hydrolase/hydrolase inhibitor Chain: Y: PDB Molecule:peptide e-76; PDBTitle: crystal structure of the complex between the peptide exosite inhibitor2 e-76 and coagulation factor viia 19 c1dvaX_ 9.3 50 PDB header:hydrolase/hydrolase inhibitor Chain: X: PDB Molecule:peptide e-76; PDBTitle: crystal structure of the complex between the peptide exosite inhibitor2 e-76 and coagulation factor viia 20 c2retE_ 8.9 15 PDB header:protein transport Chain: E: PDB Molecule:pseudopilin epsi; PDBTitle: the crystal structure of a binary complex of two pseudopilins: epsi2 and epsj from the type 2 secretion system of vibrio vulnificus 21 c2ysbA_ not modelled 8.1 20 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) 22 d1tk7a2 not modelled 7.6 13 Fold:WW domain-like Superfamily:WW domain Family:WW domain 23 d2jmfa1 not modelled 7.5 15 Fold:WW domain-like Superfamily:WW domain Family:WW domain 24 d1is3a_ not modelled 7.5 8 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Galectin (animal S-lectin) 25 c1yiuA_ not modelled 7.3 13 PDB header:ligase Chain: A: PDB Molecule:itchy e3 ubiquitin protein ligase; PDBTitle: itch e3 ubiquitin ligase ww3 domain 26 d1k9ra_ not modelled 7.1 20 Fold:WW domain-like Superfamily:WW domain Family:WW domain 27 d2e9ia1 not modelled 7.0 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Filamin repeat (rod domain) 28 d2cs3a1 not modelled 6.8 20 Fold:RING/U-box Superfamily:RING/U-box Family:Variant RING domain 29 c2yshA_ not modelled 6.5 18 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 30 c2y69Z_ not modelled 6.3 8 PDB header:electron transport Chain: Z: PDB Molecule:cytochrome c oxidase polypeptide 8h; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 31 c3a0hl_ not modelled 6.3 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 32 c3a0hL_ not modelled 6.3 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 33 c1wr7A_ not modelled 6.3 13 PDB header:ligase Chain: A: PDB Molecule:nedd4-2; PDBTitle: solution structure of the third ww domain of nedd4-2 34 c3a0bl_ not modelled 6.2 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 35 c3a0bL_ not modelled 6.2 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 36 c2lawA_ not modelled 6.0 23 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 37 d2axtl1 not modelled 6.0 30 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 38 c1s5lL_ not modelled 6.0 30 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 39 c1s5ll_ not modelled 6.0 30 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 40 c2axtL_ not modelled 6.0 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 41 c2axtl_ not modelled 6.0 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 42 c3bz1L_ not modelled 6.0 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 43 c3arcL_ not modelled 6.0 30 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 44 c3prqL_ not modelled 6.0 30 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 45 c3kziL_ not modelled 6.0 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 46 c3prrL_ not modelled 6.0 30 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 47 c3bz2L_ not modelled 6.0 30 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 48 d2ysca1 not modelled 6.0 15 Fold:WW domain-like Superfamily:WW domain Family:WW domain 49 c3u5eL_ not modelled 5.9 35 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 50 c3arcl_ not modelled 5.6 30 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 51 c2dmvA_ not modelled 5.6 18 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) 52 c2ez5W_ not modelled 5.5 13 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 53 c2djyA_ not modelled 5.4 20 PDB header:ligase/signaling protein Chain: A: PDB Molecule:smad ubiquitination regulatory factor 2; PDBTitle: solution structure of smurf2 ww3 domain-smad7 py peptide2 complex 54 c2wsfG_ not modelled 5.4 25 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i 55 c2yscA_ not modelled 5.3 15 PDB header:protein binding Chain: A: PDB Molecule:amyloid beta a4 precursor protein-binding family PDBTitle: solution structure of the ww domain from the human amyloid2 beta a4 precursor protein-binding family b member 3, apbb3

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