Secondary structure and disorder prediction

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Sequence		M	S	F	M	V	S	E	E	V	T	V	K	E	G	G	P	R	M	I	V	T	G	Y	S	S	G	M	V	E	C	R	W	Y	D	G	Y	G	V	K	R	E	A	F	H	E	T	E	L	V	P	G	E	G	S	R	S	A	E	E	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?				?	?																																		?				?	?	?		?	?	?	?	?	?	?
Disorder confidence
Sequence
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 1d1h chain A Region: 29 - 35 Aligned: 7 Modelled: 7 Confidence: 12.7% Identity: 57% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Spider toxins Phyre2 PDB 2i5y chain R Region: 5 - 33 Aligned: 29 Modelled: 29 Confidence: 12.7% Identity: 17% PDB header:virus/viral protein/immune system Chain: R: PDB Molecule:antibody 17b heavy chain; PDBTitle: crystal structure of cd4m47, a scorpion-toxin mimic of cd4, in complex2 with hiv-1 yu2 gp120 envelope glycoprotein and anti-hiv-1 antibody3 17b Phyre2 PDB 1mqt chain A Region: 9 - 37 Aligned: 29 Modelled: 29 Confidence: 12.4% Identity: 38% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Picornaviridae-like VP (VP1, VP2, VP3 and VP4) Phyre2 PDB 1pft chain A Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 10.9% Identity: 15% Fold: Rubredoxin-like Superfamily: Zinc beta-ribbon Family: Transcriptional factor domain Phyre2 PDB 1cz8 chain H Region: 3 - 33 Aligned: 31 Modelled: 31 Confidence: 10.9% Identity: 23% PDB header:immune system Chain: H: PDB Molecule:heavy chain of neutralizing antibody; PDBTitle: vascular endothelial growth factor in complex with an2 affinity matured antibody Phyre2 PDB 1xbw chain A Region: 1 - 14 Aligned: 14 Modelled: 14 Confidence: 8.7% Identity: 36% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: PG130-like Phyre2 PDB 2aq2 chain A domain 1 Region: 7 - 33 Aligned: 27 Modelled: 27 Confidence: 7.4% Identity: 11% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2o1u chain A Region: 2 - 11 Aligned: 10 Modelled: 10 Confidence: 6.9% Identity: 40% PDB header:chaperone Chain: A: PDB Molecule:endoplasmin; PDBTitle: structure of full length grp94 with amp-pnp bound Phyre2 PDB 2a1h chain A domain 1 Region: 23 - 50 Aligned: 22 Modelled: 28 Confidence: 6.9% Identity: 23% Fold: D-aminoacid aminotransferase-like PLP-dependent enzymes Superfamily: D-aminoacid aminotransferase-like PLP-dependent enzymes Family: D-aminoacid aminotransferase-like PLP-dependent enzymes Phyre2 PDB 2xk0 chain A Region: 28 - 35 Aligned: 8 Modelled: 8 Confidence: 6.3% Identity: 38% PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) Phyre2 PDB 2qqr chain A domain 2 Region: 27 - 35 Aligned: 9 Modelled: 9 Confidence: 5.8% Identity: 56% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: Tudor domain Phyre2 PDB 2qqs chain A domain 2 Region: 27 - 35 Aligned: 9 Modelled: 9 Confidence: 5.7% Identity: 56% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: Tudor domain Phyre2 PDB 1uh6 chain A Region: 13 - 20 Aligned: 8 Modelled: 8 Confidence: 5.7% Identity: 50% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 1tiu chain A Region: 7 - 35 Aligned: 29 Modelled: 29 Confidence: 5.5% Identity: 21% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 PDB 2hug chain A domain 1 Region: 30 - 35 Aligned: 6 Modelled: 6 Confidence: 5.4% Identity: 67% Fold: SH3-like barrel Superfamily: Chromo domain-like Family: Chromo domain Phyre2 PDB 2oqj chain B Region: 6 - 33 Aligned: 28 Modelled: 28 Confidence: 5.2% Identity: 25% PDB header:immune system Chain: B: PDB Molecule:fab 2g12 heavy chain; PDBTitle: crystal structure analysis of fab 2g12 in complex with peptide 2g12.1 Phyre2 1 d1d1ha_ 2 c2i5yR_ 3 d1mqta_ 4 d1pfta_ 5 c1cz8H_ 6 d1xbwa_ 7 d2aq2a1 8 c2o1uA_ 9 d2a1ha1 10 c2xk0A_ 11 d2qqra2 12 d2qqsa2 13 d1uh6a_ 14 d1tiua_ 15 d2huga1 16 c2oqjB_

Detailed template information

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

1 d1d1ha_ 12.7 57 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins 2 c2i5yR_ 12.7 17 PDB header:virus/viral protein/immune system Chain: R: PDB Molecule:antibody 17b heavy chain; PDBTitle: crystal structure of cd4m47, a scorpion-toxin mimic of cd4, in complex2 with hiv-1 yu2 gp120 envelope glycoprotein and anti-hiv-1 antibody3 17b 3 d1mqta_ 12.4 38 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Picornaviridae-like VP (VP1, VP2, VP3 and VP4) 4 d1pfta_ 10.9 15 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 5 c1cz8H_ 10.9 23 PDB header:immune system Chain: H: PDB Molecule:heavy chain of neutralizing antibody; PDBTitle: vascular endothelial growth factor in complex with an2 affinity matured antibody 6 d1xbwa_ 8.7 36 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PG130-like 7 d2aq2a1 7.4 11 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 8 c2o1uA_ 6.9 40 PDB header:chaperone Chain: A: PDB Molecule:endoplasmin; PDBTitle: structure of full length grp94 with amp-pnp bound 9 d2a1ha1 6.9 23 Fold:D-aminoacid aminotransferase-like PLP-dependent enzymes Superfamily:D-aminoacid aminotransferase-like PLP-dependent enzymes Family:D-aminoacid aminotransferase-like PLP-dependent enzymes 10 c2xk0A_ 6.3 38 PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) 11 d2qqra2 5.8 56 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 12 d2qqsa2 5.7 56 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 13 d1uh6a_ 5.7 50 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 14 d1tiua_ 5.5 21 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 15 d2huga1 5.4 67 Fold:SH3-like barrel Superfamily:Chromo domain-like Family:Chromo domain 16 c2oqjB_ 5.2 25 PDB header:immune system Chain: B: PDB Molecule:fab 2g12 heavy chain; PDBTitle: crystal structure analysis of fab 2g12 in complex with peptide 2g12.1

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