Secondary structure and disorder prediction

1

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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

M

R

V

K

R

W

L

L

A

G

I

A

L

C

L

L

T

G

M

R

D

P

F

K

P

P

E

D

L

C

R

I

S

E

L

S

Q

W

R

Y

Q

G

M

V

G

R

G

E

R

I

I

G

V

I

K

D

G

Q

K

K

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

W

R

R

V

Q

Q

N

D

V

L

E

N

G

W

T

I

L

Q

L

T

P

D

V

L

T

L

G

T

G

T

N

C

E

P

P

Q

W

L

W

Q

R

Q

G

D

T

N

E

A

M

D

S

R

T

T

V

D

A

D

T

R

Secondary structure

SS confidence

Disorder

?

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?

Disorder confidence

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130

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Sequence

R

T

G

G

K

A

A

K

S

D

A

D

G

G

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

Rank Aligned region

PDB 2ivw chain A Region: 17 - 92 Aligned: 75 Modelled: 76 Confidence: 96.7% Identity: 21% PDB header:lipoprotein Chain: A: PDB Molecule:pilp pilot protein; PDBTitle: the solution structure of a domain from the neisseria2 meningitidis pilp pilot protein. Phyre2 PDB 2lc4 chain A Region: 23 - 92 Aligned: 69 Modelled: 70 Confidence: 96.5% Identity: 14% PDB header:structural protein Chain: A: PDB Molecule:pilp protein; PDBTitle: solution structure of pilp from pseudomonas aeruginosa Phyre2 PDB 3oss chain C Region: 39 - 87 Aligned: 47 Modelled: 49 Confidence: 83.8% Identity: 19% PDB header:protein transport Chain: C: PDB Molecule:type 2 secretion system, gspc; PDBTitle: the crystal structure of enterotoxigenic escherichia coli gspc-gspd2 complex from the type ii secretion system Phyre2 PDB 2r6g chain F domain 1 Region: 53 - 77 Aligned: 25 Modelled: 25 Confidence: 22.5% Identity: 16% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 2e61 chain A Region: 42 - 74 Aligned: 33 Modelled: 33 Confidence: 16.4% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:zinc finger cw-type pwwp domain protein 1; PDBTitle: solution structure of the zf-cw domain in zinc finger cw-type pwwp2 domain protein 1 Phyre2 PDB 2jh3 chain C Region: 56 - 84 Aligned: 28 Modelled: 29 Confidence: 12.4% Identity: 32% PDB header:ribosomal protein Chain: C: PDB Molecule:ribosomal protein s2-related protein; PDBTitle: the crystal structure of dr2241 from deinococcus2 radiodurans at 1.9 a resolution reveals a multi-domain3 protein with structural similarity to chelatases but also4 with two additional novel domains Phyre2 PDB 1rk8 chain C Region: 46 - 65 Aligned: 20 Modelled: 20 Confidence: 12.4% Identity: 20% PDB header:translation Chain: C: PDB Molecule:within the bgcn gene intron protein; PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex Phyre2 PDB 1rk8 chain C Region: 46 - 65 Aligned: 20 Modelled: 20 Confidence: 12.4% Identity: 20% Fold: WW domain-like Superfamily: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Family: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Phyre2 PDB 2f1z chain B Region: 25 - 119 Aligned: 88 Modelled: 95 Confidence: 10.9% Identity: 13% PDB header:hydrolase Chain: B: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 7; PDBTitle: crystal structure of hausp Phyre2 PDB 2hd5 chain A domain 1 Region: 39 - 64 Aligned: 26 Modelled: 26 Confidence: 10.6% Identity: 8% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Ubiquitin carboxyl-terminal hydrolase, UCH Phyre2 PDB 2ayn chain A domain 1 Region: 21 - 69 Aligned: 49 Modelled: 49 Confidence: 9.7% Identity: 16% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Ubiquitin carboxyl-terminal hydrolase, UCH Phyre2 PDB 3mhs chain A Region: 39 - 63 Aligned: 25 Modelled: 25 Confidence: 9.0% Identity: 24% PDB header:hydrolase/transcription regulator/protei Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 8; PDBTitle: structure of the saga ubp8/sgf11/sus1/sgf73 dub module bound to2 ubiquitin aldehyde Phyre2 PDB 2f21 chain A domain 1 Region: 70 - 76 Aligned: 7 Modelled: 7 Confidence: 8.7% Identity: 43% Fold: WW domain-like Superfamily: WW domain Family: WW domain Phyre2 PDB 2itk chain A domain 1 Region: 70 - 76 Aligned: 7 Modelled: 7 Confidence: 8.2% Identity: 43% Fold: WW domain-like Superfamily: WW domain Family: WW domain Phyre2 PDB 1xak chain A Region: 22 - 28 Aligned: 7 Modelled: 7 Confidence: 8.1% Identity: 57% Fold: Immunoglobulin-like beta-sandwich Superfamily: Accessory protein X4 (ORF8, ORF7a) Family: Accessory protein X4 (ORF8, ORF7a) Phyre2 PDB 2laz chain A Region: 70 - 76 Aligned: 7 Modelled: 7 Confidence: 7.8% Identity: 29% 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 2lb0 chain A Region: 70 - 76 Aligned: 7 Modelled: 7 Confidence: 7.8% Identity: 29% 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 Phyre2 PDB 2ysc chain A domain 1 Region: 70 - 91 Aligned: 22 Modelled: 22 Confidence: 7.7% Identity: 14% Fold: WW domain-like Superfamily: WW domain Family: WW domain Phyre2 PDB 2kq0 chain A Region: 69 - 76 Aligned: 8 Modelled: 8 Confidence: 7.5% Identity: 38% 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 1tg7 chain A domain 2 Region: 38 - 49 Aligned: 12 Modelled: 12 Confidence: 7.0% Identity: 25% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Beta-galactosidase LacA, domains 4 and 5 Phyre2 1 c2ivwA_ 2 c2lc4A_ 3 c3ossC_ 4 d2r6gf1 5 c2e61A_ 6 c2jh3C_ 7 c1rk8C_ 8 d1rk8c_ 9 c2f1zB_ 10 d2hd5a1 11 d2ayna1 12 c3mhsA_ 13 d2f21a1 14 d2itka1 15 d1xaka_ 16 c2lazA_ 17 c2lb0A_ 18 d2ysca1 19 c2kq0A_ 20 d1tg7a2 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 c2ivwA_ 96.7 21 PDB header:lipoprotein Chain: A: PDB Molecule:pilp pilot protein; PDBTitle: the solution structure of a domain from the neisseria2 meningitidis pilp pilot protein. 2 c2lc4A_ 96.5 14 PDB header:structural protein Chain: A: PDB Molecule:pilp protein; PDBTitle: solution structure of pilp from pseudomonas aeruginosa 3 c3ossC_ 83.8 19 PDB header:protein transport Chain: C: PDB Molecule:type 2 secretion system, gspc; PDBTitle: the crystal structure of enterotoxigenic escherichia coli gspc-gspd2 complex from the type ii secretion system 4 d2r6gf1 22.5 16 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 5 c2e61A_ 16.4 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:zinc finger cw-type pwwp domain protein 1; PDBTitle: solution structure of the zf-cw domain in zinc finger cw-type pwwp2 domain protein 1 6 c2jh3C_ 12.4 32 PDB header:ribosomal protein Chain: C: PDB Molecule:ribosomal protein s2-related protein; PDBTitle: the crystal structure of dr2241 from deinococcus2 radiodurans at 1.9 a resolution reveals a multi-domain3 protein with structural similarity to chelatases but also4 with two additional novel domains 7 c1rk8C_ 12.4 20 PDB header:translation Chain: C: PDB Molecule:within the bgcn gene intron protein; PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex 8 d1rk8c_ 12.4 20 Fold:WW domain-like Superfamily:Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Family:Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain 9 c2f1zB_ 10.9 13 PDB header:hydrolase Chain: B: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 7; PDBTitle: crystal structure of hausp 10 d2hd5a1 10.6 8 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Ubiquitin carboxyl-terminal hydrolase, UCH 11 d2ayna1 9.7 16 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Ubiquitin carboxyl-terminal hydrolase, UCH 12 c3mhsA_ 9.0 24 PDB header:hydrolase/transcription regulator/protei Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 8; PDBTitle: structure of the saga ubp8/sgf11/sus1/sgf73 dub module bound to2 ubiquitin aldehyde 13 d2f21a1 8.7 43 Fold:WW domain-like Superfamily:WW domain Family:WW domain 14 d2itka1 8.2 43 Fold:WW domain-like Superfamily:WW domain Family:WW domain 15 d1xaka_ 8.1 57 Fold:Immunoglobulin-like beta-sandwich Superfamily:Accessory protein X4 (ORF8, ORF7a) Family:Accessory protein X4 (ORF8, ORF7a) 16 c2lazA_ 7.8 29 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 17 c2lb0A_ 7.8 29 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 18 d2ysca1 7.7 14 Fold:WW domain-like Superfamily:WW domain Family:WW domain 19 c2kq0A_ 7.5 38 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 20 d1tg7a2 7.0 25 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Beta-galactosidase LacA, domains 4 and 5 21 c3h6sE_ not modelled 6.7 13 PDB header:hydrolase/hydrolase inhibitor Chain: E: PDB Molecule:clitocypin analog; PDBTitle: strucure of clitocypin - cathepsin v complex 22 d1pina1 not modelled 6.7 43 Fold:WW domain-like Superfamily:WW domain Family:WW domain 23 d2jmfa1 not modelled 6.6 57 Fold:WW domain-like Superfamily:WW domain Family:WW domain 24 c1yo4A_ not modelled 6.5 57 PDB header:viral protein Chain: A: PDB Molecule:hypothetical protein x4; PDBTitle: solution structure of the sars coronavirus orf 7a coded x42 protein 25 d1w9sa_ not modelled 6.3 11 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 6 carbohydrate binding module, CBM6 26 d1hk9a_ not modelled 6.1 12 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 27 c2jv4A_ not modelled 5.8 43 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 28 d1ft8e_ not modelled 5.7 45 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Non-canonical RBD domain 29 c2ysfA_ not modelled 5.7 43 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 30 d2gpfa1 not modelled 5.6 8 Fold:MbtH/L9 domain-like Superfamily:MbtH-like Family:MbtH-like 31 c2jmfA_ not modelled 5.6 25 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 32 c2khrA_ not modelled 5.5 8 PDB header:biosynthetic protein Chain: A: PDB Molecule:protein mbth; PDBTitle: solution structure of rv2377c, a mbth-like protein from mycobacterium2 tuberculosis 33 c3qhsD_ not modelled 5.5 12 PDB header:rna binding protein Chain: D: PDB Molecule:protein hfq; PDBTitle: crystal structure of full-length hfq from escherichia coli 34 d2pstx1 not modelled 5.2 8 Fold:MbtH/L9 domain-like Superfamily:MbtH-like Family:MbtH-like

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

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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