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

L

Q

E

E

L

C

S

V

V

E

A

S

G

A

S

L

E

K

G

R

H

D

Q

L

L

T

A

L

R

A

L

L

L

S

R

K

N

P

F

G

D

I

K

L

D

G

T

V

Q

K

A

L

E

N

L

G

L

G

E

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

A

A

K

R

N

V

G

T

G

A

N

Q

I

P

D

M

G

S

F

M

L

S

A

S

V

P

G

Y

Q

K

L

P

S

G

L

I

I

Q

W

G

P

I

D

V

P

L

T

S

Q

D

T

V

T

Y

F

P

I

A

F

P

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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Sequence

N

R

C

L

R

V

F

A

T

Q

D

Y

T

P

G

S

A

N

V

G

Y

I

A

C

A

G

Y

N

Q

D

P

V

K

F

I

S

R

A

G

V

P

G

I

G

A

S

F

F

A

L

G

C

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 2ccv chain A domain 1 Region: 99 - 170 Aligned: 72 Modelled: 72 Confidence: 82.1% Identity: 10% Fold: HPA-like Superfamily: Agglutinin HPA-like Family: Agglutinin HPA-like Phyre2 PDB 2vme chain C Region: 105 - 170 Aligned: 66 Modelled: 66 Confidence: 37.0% Identity: 11% PDB header:cell adhesion Chain: C: PDB Molecule:discoidin-2; PDBTitle: structure of the wild-type discoidin ii from dictyostelium2 discoideum Phyre2 PDB 2w95 chain B Region: 111 - 171 Aligned: 61 Modelled: 61 Confidence: 26.8% Identity: 16% 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 Phyre2 PDB 3a1y chain F Region: 4 - 29 Aligned: 26 Modelled: 26 Confidence: 25.3% Identity: 38% PDB header:ribosomal protein Chain: F: PDB Molecule:50s ribosomal protein p1 (l12p); PDBTitle: the structure of protein complex Phyre2 PDB 3hrz chain A Region: 88 - 133 Aligned: 46 Modelled: 46 Confidence: 13.7% Identity: 15% PDB header:immune system Chain: A: PDB Molecule:cobra venom factor; PDBTitle: cobra venom factor (cvf) in complex with human factor b Phyre2 PDB 2w1o chain A Region: 3 - 47 Aligned: 45 Modelled: 45 Confidence: 12.1% Identity: 9% PDB header:translation Chain: A: PDB Molecule:60s acidic ribosomal protein p2; PDBTitle: nmr structure of dimerization domain of human ribosomal2 protein p2 Phyre2 PDB 3p45 chain F Region: 4 - 38 Aligned: 32 Modelled: 35 Confidence: 12.1% Identity: 22% PDB header:hydrolase Chain: F: PDB Molecule:caspase-6; PDBTitle: crystal structure of apo-caspase-6 at physiological ph Phyre2 PDB 3trk chain A Region: 6 - 30 Aligned: 25 Modelled: 25 Confidence: 11.6% Identity: 24% PDB header:hydrolase Chain: A: PDB Molecule:nonstructural polyprotein; PDBTitle: structure of the chikungunya virus nsp2 protease Phyre2 PDB 1jqp chain A domain 2 Region: 76 - 120 Aligned: 36 Modelled: 45 Confidence: 10.4% Identity: 17% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Papain-like Phyre2 PDB 1ev0 chain A Region: 1 - 12 Aligned: 12 Modelled: 12 Confidence: 9.3% Identity: 17% Fold: Cell division protein MinE topological specificity domain Superfamily: Cell division protein MinE topological specificity domain Family: Cell division protein MinE topological specificity domain Phyre2 PDB 2jsn chain A Region: 92 - 119 Aligned: 27 Modelled: 28 Confidence: 9.2% Identity: 7% PDB header:protein transport Chain: A: PDB Molecule:trafficking protein particle complex subunit 4; PDBTitle: solution structure of the atypical pdz-like domain of2 synbindin Phyre2 PDB 1bqf chain A Region: 85 - 94 Aligned: 10 Modelled: 10 Confidence: 9.0% Identity: 50% PDB header:hormone/growth factor Chain: A: PDB Molecule:protein (growth-blocking peptide); PDBTitle: growth-blocking peptide (gbp) from pseudaletia separata Phyre2 PDB 1aoy chain A Region: 3 - 15 Aligned: 13 Modelled: 13 Confidence: 8.2% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Arginine repressor (ArgR), N-terminal DNA-binding domain Phyre2 PDB 2ct8 chain A Region: 111 - 126 Aligned: 16 Modelled: 16 Confidence: 7.8% Identity: 19% PDB header:ligase/rna Chain: A: PDB Molecule:methionyl-trna synthetase; PDBTitle: crystal structure of aquifex aeolicus methionyl-trna2 synthetase complexed with trna(met) and methionyl-adenylate3 anologue Phyre2 PDB 2p5k chain A domain 1 Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 7.8% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Arginine repressor (ArgR), N-terminal DNA-binding domain Phyre2 PDB 1f9n chain A domain 1 Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 7.4% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Arginine repressor (ArgR), N-terminal DNA-binding domain Phyre2 PDB 1fd9 chain A Region: 5 - 121 Aligned: 114 Modelled: 117 Confidence: 7.2% Identity: 15% Fold: FKBP-like Superfamily: FKBP-like Family: FKBP immunophilin/proline isomerase Phyre2 PDB 2kxw chain B Region: 3 - 10 Aligned: 8 Modelled: 8 Confidence: 7.1% Identity: 50% PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 Phyre2 PDB 1b4a chain A domain 1 Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 6.3% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Arginine repressor (ArgR), N-terminal DNA-binding domain Phyre2 PDB 1b4a chain A Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 6.0% Identity: 29% PDB header:repressor Chain: A: PDB Molecule:arginine repressor; PDBTitle: structure of the arginine repressor from bacillus stearothermophilus Phyre2 1 d2ccva1 2 c2vmeC_ 3 c2w95B_ 4 c3a1yF_ 5 c3hrzA_ 6 c2w1oA_ 7 c3p45F_ 8 c3trkA_ 9 d1jqpa2 10 d1ev0a_ 11 c2jsnA_ 12 c1bqfA_ 13 d1aoya_ 14 c2ct8A_ 15 d2p5ka1 16 d1f9na1 17 d1fd9a_ 18 c2kxwB_ 19 d1b4aa1 20 c1b4aA_ 21 22 23 24 25

Detailed template information

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

1 d2ccva1 82.1 10 Fold:HPA-like Superfamily:Agglutinin HPA-like Family:Agglutinin HPA-like 2 c2vmeC_ 37.0 11 PDB header:cell adhesion Chain: C: PDB Molecule:discoidin-2; PDBTitle: structure of the wild-type discoidin ii from dictyostelium2 discoideum 3 c2w95B_ 26.8 16 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 4 c3a1yF_ 25.3 38 PDB header:ribosomal protein Chain: F: PDB Molecule:50s ribosomal protein p1 (l12p); PDBTitle: the structure of protein complex 5 c3hrzA_ 13.7 15 PDB header:immune system Chain: A: PDB Molecule:cobra venom factor; PDBTitle: cobra venom factor (cvf) in complex with human factor b 6 c2w1oA_ 12.1 9 PDB header:translation Chain: A: PDB Molecule:60s acidic ribosomal protein p2; PDBTitle: nmr structure of dimerization domain of human ribosomal2 protein p2 7 c3p45F_ 12.1 22 PDB header:hydrolase Chain: F: PDB Molecule:caspase-6; PDBTitle: crystal structure of apo-caspase-6 at physiological ph 8 c3trkA_ 11.6 24 PDB header:hydrolase Chain: A: PDB Molecule:nonstructural polyprotein; PDBTitle: structure of the chikungunya virus nsp2 protease 9 d1jqpa2 10.4 17 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Papain-like 10 d1ev0a_ 9.3 17 Fold:Cell division protein MinE topological specificity domain Superfamily:Cell division protein MinE topological specificity domain Family:Cell division protein MinE topological specificity domain 11 c2jsnA_ 9.2 7 PDB header:protein transport Chain: A: PDB Molecule:trafficking protein particle complex subunit 4; PDBTitle: solution structure of the atypical pdz-like domain of2 synbindin 12 c1bqfA_ 9.0 50 PDB header:hormone/growth factor Chain: A: PDB Molecule:protein (growth-blocking peptide); PDBTitle: growth-blocking peptide (gbp) from pseudaletia separata 13 d1aoya_ 8.2 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 14 c2ct8A_ 7.8 19 PDB header:ligase/rna Chain: A: PDB Molecule:methionyl-trna synthetase; PDBTitle: crystal structure of aquifex aeolicus methionyl-trna2 synthetase complexed with trna(met) and methionyl-adenylate3 anologue 15 d2p5ka1 7.8 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 16 d1f9na1 7.4 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 17 d1fd9a_ 7.2 15 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 18 c2kxwB_ 7.1 50 PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 19 d1b4aa1 6.3 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 20 c1b4aA_ 6.0 29 PDB header:repressor Chain: A: PDB Molecule:arginine repressor; PDBTitle: structure of the arginine repressor from bacillus stearothermophilus 21 c1dfwA_ not modelled 6.0 67 PDB header:immune system Chain: A: PDB Molecule:lung surfactant protein b; PDBTitle: conformational mapping of the n-terminal segment of2 surfactant protein b in lipid using 13c-enhanced fourier3 transform infrared spectroscopy (ftir) 22 d2sici_ not modelled 5.7 19 Fold:Subtilisin inhibitor Superfamily:Subtilisin inhibitor Family:Subtilisin inhibitor 23 d2hgsa4 not modelled 5.5 40 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:Eukaryotic glutathione synthetase ATP-binding domain 24 c2xvcA_ not modelled 5.4 10 PDB header:cell cycle Chain: A: PDB Molecule:escrt-iii; PDBTitle: molecular and structural basis of escrt-iii recruitment to2 membranes during archaeal cell division 25 d1m0wa2 not modelled 5.4 30 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:Eukaryotic glutathione synthetase ATP-binding domain

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