Secondary structure and disorder prediction

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Sequence		M	S	A	G	V	I	T	G	V	L	L	V	F	L	L	L	G	Y	L	V	Y	A	L	I	N	A	E	A	F
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 2l9u chain A Region: 1 - 17 Aligned: 17 Modelled: 17 Confidence: 38.0% Identity: 41% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain Phyre2 PDB 1i2t chain A Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 20.5% Identity: 67% Fold: PABP domain-like Superfamily: PABC (PABP) domain Family: PABC (PABP) domain Phyre2 PDB 3pth chain A Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 20.3% Identity: 78% PDB header:rna binding protein Chain: A: PDB Molecule:polyadenylate-binding protein 1; PDBTitle: the pabc1 mlle domain bound to the variant pam2 motif of larp4b Phyre2 PDB 2dyd chain A Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 20.0% Identity: 45% PDB header:rna binding protein Chain: A: PDB Molecule:poly(a)-binding protein; PDBTitle: solution structure of the pabc domain from triticum2 aevestium poly(a)-binding protein Phyre2 PDB 1ifw chain A Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 18.8% Identity: 67% Fold: PABP domain-like Superfamily: PABC (PABP) domain Family: PABC (PABP) domain Phyre2 PDB 1nmr chain A Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 13.3% Identity: 56% Fold: PABP domain-like Superfamily: PABC (PABP) domain Family: PABC (PABP) domain Phyre2 PDB 2e74 chain G domain 1 Region: 11 - 22 Aligned: 12 Modelled: 12 Confidence: 12.3% Identity: 67% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 1jgn chain A Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 12.2% Identity: 78% Fold: PABP domain-like Superfamily: PABC (PABP) domain Family: PABC (PABP) domain Phyre2 PDB 2l35 chain B Region: 1 - 20 Aligned: 20 Modelled: 20 Confidence: 12.1% Identity: 35% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 2l2t chain A Region: 3 - 21 Aligned: 19 Modelled: 19 Confidence: 11.7% Identity: 53% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 2l34 chain A Region: 1 - 20 Aligned: 20 Modelled: 20 Confidence: 11.4% Identity: 35% PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 2l34 chain B Region: 1 - 20 Aligned: 20 Modelled: 20 Confidence: 11.4% Identity: 35% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 1vf5 chain G Region: 11 - 22 Aligned: 12 Modelled: 12 Confidence: 11.1% Identity: 67% PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 1vf5 chain G Region: 11 - 22 Aligned: 12 Modelled: 12 Confidence: 11.1% Identity: 67% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 PDB 2y69 chain Q Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 12% PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1g9l chain A Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 7.6% Identity: 78% Fold: PABP domain-like Superfamily: PABC (PABP) domain Family: PABC (PABP) domain Phyre2 PDB 2k9y chain B Region: 4 - 17 Aligned: 14 Modelled: 14 Confidence: 6.7% Identity: 50% PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 2k9y chain A Region: 4 - 17 Aligned: 14 Modelled: 14 Confidence: 6.7% Identity: 50% PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 Phyre2 PDB 2k1k chain B Region: 5 - 21 Aligned: 17 Modelled: 17 Confidence: 6.2% Identity: 65% PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 Phyre2 PDB 2k1l chain A Region: 5 - 21 Aligned: 17 Modelled: 17 Confidence: 6.2% Identity: 65% PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 Phyre2 1 c2l9uA_ 2 d1i2ta_ 3 c3pthA_ 4 c2dydA_ 5 d1ifwa_ 6 d1nmra_ 7 d2e74g1 8 d1jgna_ 9 c2l35B_ 10 c2l2tA_ 11 c2l34A_ 12 c2l34B_ 13 c1vf5G_ 14 d1vf5g_ 15 c2y69Q_ 16 d1g9la_ 17 c2k9yB_ 18 c2k9yA_ 19 c2k1kB_ 20 c2k1lA_ 21 22 23

Detailed template information

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

1 c2l9uA_ 38.0 41 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 2 d1i2ta_ 20.5 67 Fold:PABP domain-like Superfamily:PABC (PABP) domain Family:PABC (PABP) domain 3 c3pthA_ 20.3 78 PDB header:rna binding protein Chain: A: PDB Molecule:polyadenylate-binding protein 1; PDBTitle: the pabc1 mlle domain bound to the variant pam2 motif of larp4b 4 c2dydA_ 20.0 45 PDB header:rna binding protein Chain: A: PDB Molecule:poly(a)-binding protein; PDBTitle: solution structure of the pabc domain from triticum2 aevestium poly(a)-binding protein 5 d1ifwa_ 18.8 67 Fold:PABP domain-like Superfamily:PABC (PABP) domain Family:PABC (PABP) domain 6 d1nmra_ 13.3 56 Fold:PABP domain-like Superfamily:PABC (PABP) domain Family:PABC (PABP) domain 7 d2e74g1 12.3 67 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 8 d1jgna_ 12.2 78 Fold:PABP domain-like Superfamily:PABC (PABP) domain Family:PABC (PABP) domain 9 c2l35B_ 12.1 35 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 10 c2l2tA_ 11.7 53 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 11 c2l34A_ 11.4 35 PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 12 c2l34B_ 11.4 35 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 13 c1vf5G_ 11.1 67 PDB header:photosynthesis Chain: G: PDB Molecule:protein pet g; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 14 d1vf5g_ 11.1 67 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex 15 c2y69Q_ 7.9 12 PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 16 d1g9la_ 7.6 78 Fold:PABP domain-like Superfamily:PABC (PABP) domain Family:PABC (PABP) domain 17 c2k9yB_ 6.7 50 PDB header:transferase Chain: B: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 18 c2k9yA_ 6.7 50 PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: epha2 dimeric structure in the lipidic bicelle at ph 5.0 19 c2k1kB_ 6.2 65 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 20 c2k1lA_ 6.2 65 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 21 c2k1kA_ not modelled 6.2 65 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 22 c2k1lB_ not modelled 6.2 65 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 23 d1v54d_ not modelled 6.0 12 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit IV Family:Mitochondrial cytochrome c oxidase subunit IV

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