Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	R	H	R	L	Q	H	H	G	T	C	A	N	L	R	A	A	P	N	F	N	I	A	E	D	F	R	A	R	A	N	H	H	T	F	T	N	F	R	V	T	V	T	T	R	F	T	R	T	A	K	R	H	R	L	Q	N	R	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?																																					?	?				?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	V	F	N	H	R	R	F	T	N	D	D	A	C	R	V	V	K	H	D	T	A	T	N	F	C	C	R	V	N	I	D	L	E	R	H	R	N	L	V	L	Q	K	D	C	Q	C	A	T	P	L	I	P	Q	P	V	T	D	A	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130
Sequence		G	L	Q	G	M	K	T	L	Q	V
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 2hzq chain A Region: 8 - 25 Aligned: 18 Modelled: 18 Confidence: 17.6% Identity: 33% PDB header:transport protein Chain: A: PDB Molecule:apolipoprotein d; PDBTitle: crystal structure of human apolipoprotein d (apod) in2 complex with progesterone Phyre2 PDB 1vd3 chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 14.2% Identity: 40% PDB header:hydrolase Chain: A: PDB Molecule:rnase ngr3; PDBTitle: ribonuclease nt in complex with 2'-ump Phyre2 PDB 1iyb chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 13.8% Identity: 37% Fold: Ribonuclease Rh-like Superfamily: Ribonuclease Rh-like Family: Ribonuclease Rh-like Phyre2 PDB 2pqx chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 11.2% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease i; PDBTitle: e. coli rnase 1 (in vivo folded) Phyre2 PDB 1kxo chain A Region: 10 - 24 Aligned: 15 Modelled: 15 Confidence: 10.5% Identity: 27% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 1bbp chain A Region: 8 - 27 Aligned: 19 Modelled: 20 Confidence: 10.2% Identity: 26% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 1dix chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 9.1% Identity: 30% Fold: Ribonuclease Rh-like Superfamily: Ribonuclease Rh-like Family: Ribonuclease Rh-like Phyre2 PDB 1n0s chain A Region: 8 - 24 Aligned: 17 Modelled: 17 Confidence: 8.4% Identity: 29% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 1sgl chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 8.1% Identity: 23% Fold: Ribonuclease Rh-like Superfamily: Ribonuclease Rh-like Family: Ribonuclease Rh-like Phyre2 PDB 1jy5 chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 7.5% Identity: 23% Fold: Ribonuclease Rh-like Superfamily: Ribonuclease Rh-like Family: Ribonuclease Rh-like Phyre2 PDB 1z24 chain A domain 1 Region: 9 - 25 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 18% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 1sg1 chain X domain 2 Region: 115 - 127 Aligned: 13 Modelled: 13 Confidence: 6.9% Identity: 46% Fold: TNF receptor-like Superfamily: TNF receptor-like Family: TNF receptor-like Phyre2 PDB 1gka chain B Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 5.9% Identity: 31% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 1ucd chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 5.9% Identity: 30% Fold: Ribonuclease Rh-like Superfamily: Ribonuclease Rh-like Family: Ribonuclease Rh-like Phyre2 PDB 3d3z chain A Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 5.6% Identity: 27% PDB header:hydrolase Chain: A: PDB Molecule:actibind; PDBTitle: crystal structure of actibind a t2 rnase Phyre2 PDB 2a0s chain A domain 1 Region: 4 - 15 Aligned: 12 Modelled: 12 Confidence: 5.5% Identity: 25% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: 6-pyruvoyl tetrahydropterin synthase Phyre2 PDB 1y13 chain A Region: 4 - 15 Aligned: 12 Modelled: 12 Confidence: 5.5% Identity: 25% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: 6-pyruvoyl tetrahydropterin synthase Phyre2 1 c2hzqA_ 2 c1vd3A_ 3 d1iyba_ 4 c2pqxA_ 5 d1kxoa_ 6 d1bbpa_ 7 d1dixa_ 8 d1n0sa_ 9 d1sgla_ 10 d1jy5a_ 11 d1z24a1 12 d1sg1x2 13 d1gkab_ 14 d1ucda_ 15 c3d3zA_ 16 d2a0sa1 17 d1y13a_

Detailed template information

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

1 c2hzqA_ 17.6 33 PDB header:transport protein Chain: A: PDB Molecule:apolipoprotein d; PDBTitle: crystal structure of human apolipoprotein d (apod) in2 complex with progesterone 2 c1vd3A_ 14.2 40 PDB header:hydrolase Chain: A: PDB Molecule:rnase ngr3; PDBTitle: ribonuclease nt in complex with 2'-ump 3 d1iyba_ 13.8 37 Fold:Ribonuclease Rh-like Superfamily:Ribonuclease Rh-like Family:Ribonuclease Rh-like 4 c2pqxA_ 11.2 17 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease i; PDBTitle: e. coli rnase 1 (in vivo folded) 5 d1kxoa_ 10.5 27 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 6 d1bbpa_ 10.2 26 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 7 d1dixa_ 9.1 30 Fold:Ribonuclease Rh-like Superfamily:Ribonuclease Rh-like Family:Ribonuclease Rh-like 8 d1n0sa_ 8.4 29 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 9 d1sgla_ 8.1 23 Fold:Ribonuclease Rh-like Superfamily:Ribonuclease Rh-like Family:Ribonuclease Rh-like 10 d1jy5a_ 7.5 23 Fold:Ribonuclease Rh-like Superfamily:Ribonuclease Rh-like Family:Ribonuclease Rh-like 11 d1z24a1 7.4 18 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 12 d1sg1x2 6.9 46 Fold:TNF receptor-like Superfamily:TNF receptor-like Family:TNF receptor-like 13 d1gkab_ 5.9 31 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 14 d1ucda_ 5.9 30 Fold:Ribonuclease Rh-like Superfamily:Ribonuclease Rh-like Family:Ribonuclease Rh-like 15 c3d3zA_ 5.6 27 PDB header:hydrolase Chain: A: PDB Molecule:actibind; PDBTitle: crystal structure of actibind a t2 rnase 16 d2a0sa1 5.5 25 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:6-pyruvoyl tetrahydropterin synthase 17 d1y13a_ 5.5 25 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:6-pyruvoyl tetrahydropterin synthase

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