Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	I	N	I	G	R	L	L	M	L	C	V	W	G	F	L	I	L	N	L	V	H	P	F	P	R	P	L	N	I	F	V	N	V	A	L	I	F	T	V	L	M	H	G	M	Q	L	A	L	L	K	S	T	L	P	K	D	G	P
Secondary structure
SS confidence
Disorder		?	?																																																						?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		Q	M	T	T	A	E	K	V	R	I	F	L	F	G	V	F	E	L	L	A	W	Q	K	K	F	K	V	K	K
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 3lw5 chain 2 Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 56.2% Identity: 21% PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from photosystem i; PDB Fragment:residues 81-246; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2wsf chain 2 Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 54.2% Identity: 21% PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from PDBTitle: improved model of plant photosystem i Phyre2 PDB 2wse chain 4 Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 50.6% Identity: 29% PDB header:photosynthesis Chain: 4: PDB Molecule:chlorophyll a-b binding protein p4, PDBTitle: improved model of plant photosystem i Phyre2 PDB 3pl9 chain A Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 48.6% Identity: 25% PDB header:photosynthesis Chain: A: PDB Molecule:chlorophyll a-b binding protein; PDBTitle: crystal structure of spinach minor light-harvesting complex cp29 at2 2.80 angstrom resolution Phyre2 PDB 1rwt chain A Region: 3 - 22 Aligned: 20 Modelled: 20 Confidence: 48.3% Identity: 40% Fold: Chlorophyll a-b binding protein Superfamily: Chlorophyll a-b binding protein Family: Chlorophyll a-b binding protein Phyre2 PDB 2wse chain 3 Region: 3 - 17 Aligned: 15 Modelled: 15 Confidence: 36.3% Identity: 40% PDB header:photosynthesis Chain: 3: PDB Molecule:lhca3; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2o01 chain 1 Region: 3 - 18 Aligned: 16 Modelled: 16 Confidence: 35.0% Identity: 44% PDB header:photosynthesis Chain: 1: PDB Molecule:at3g54890; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2o01 chain 4 Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 34.4% Identity: 29% PDB header:photosynthesis Chain: 4: PDB Molecule:psi light-harvesting antenna chlorophyll a/b- PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2o01 chain 2 Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 31.9% Identity: 21% PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 3brv chain B Region: 77 - 89 Aligned: 13 Modelled: 13 Confidence: 31.3% Identity: 38% PDB header:transferase/transcription Chain: B: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo/ikkb association domain structure Phyre2 PDB 1afo chain B Region: 21 - 45 Aligned: 20 Modelled: 25 Confidence: 31.2% Identity: 40% PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures Phyre2 PDB 2o01 chain 3 Region: 3 - 18 Aligned: 16 Modelled: 16 Confidence: 24.1% Identity: 44% PDB header:photosynthesis Chain: 3: PDB Molecule:psi type iii chlorophyll a/b-binding protein; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2wsc chain 1 Region: 3 - 18 Aligned: 16 Modelled: 16 Confidence: 19.9% Identity: 44% PDB header:photosynthesis Chain: 1: PDB Molecule:at3g54890; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2q7c chain C Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 12.7% Identity: 64% PDB header:viral protein Chain: C: PDB Molecule:fusion protein between yeast variant gcn4 and PDBTitle: crystal structure of iqn17 Phyre2 PDB 2h3o chain A Region: 70 - 81 Aligned: 12 Modelled: 12 Confidence: 8.4% Identity: 42% PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices Phyre2 PDB 1waz chain A Region: 70 - 81 Aligned: 12 Modelled: 12 Confidence: 8.1% Identity: 42% PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles Phyre2 PDB 2vxo chain B Region: 23 - 28 Aligned: 6 Modelled: 6 Confidence: 7.5% Identity: 83% PDB header:ligase Chain: B: PDB Molecule:gmp synthase [glutamine-hydrolyzing]; PDBTitle: human gmp synthetase in complex with xmp Phyre2 PDB 3cyo chain A Region: 8 - 15 Aligned: 8 Modelled: 8 Confidence: 6.6% Identity: 75% PDB header:viral protein Chain: A: PDB Molecule:transmembrane protein; PDBTitle: structure of a longer thermalstable core domain of hiv-12 gp41 containing the enfuvirtide resistance mutation n43d3 and complementary mutation e137k Phyre2 PDB 3o3z chain A Region: 8 - 15 Aligned: 8 Modelled: 8 Confidence: 5.7% Identity: 75% PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein gp160; PDBTitle: complex of a chimeric alpha/beta-peptide based on the gp41 chr domain2 bound to a gp41 nhr domain peptide Phyre2 PDB 3uow chain B Region: 23 - 28 Aligned: 6 Modelled: 6 Confidence: 5.7% Identity: 83% PDB header:ligase Chain: B: PDB Molecule:gmp synthetase; PDBTitle: crystal structure of pf10_0123, a gmp synthetase from plasmodium2 falciparum Phyre2 1 c3lw52_ 2 c2wsf2_ 3 c2wse4_ 4 c3pl9A_ 5 d1rwta_ 6 c2wse3_ 7 c2o011_ 8 c2o014_ 9 c2o012_ 10 c3brvB_ 11 c1afoB_ 12 c2o013_ 13 c2wsc1_ 14 c2q7cC_ 15 c2h3oA_ 16 c1wazA_ 17 c2vxoB_ 18 c3cyoA_ 19 c3o3zA_ 20 c3uowB_ 21

Detailed template information

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

1 c3lw52_ 56.2 21 PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from photosystem i; PDB Fragment:residues 81-246; PDBTitle: improved model of plant photosystem i 2 c2wsf2_ 54.2 21 PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from PDBTitle: improved model of plant photosystem i 3 c2wse4_ 50.6 29 PDB header:photosynthesis Chain: 4: PDB Molecule:chlorophyll a-b binding protein p4, PDBTitle: improved model of plant photosystem i 4 c3pl9A_ 48.6 25 PDB header:photosynthesis Chain: A: PDB Molecule:chlorophyll a-b binding protein; PDBTitle: crystal structure of spinach minor light-harvesting complex cp29 at2 2.80 angstrom resolution 5 d1rwta_ 48.3 40 Fold:Chlorophyll a-b binding protein Superfamily:Chlorophyll a-b binding protein Family:Chlorophyll a-b binding protein 6 c2wse3_ 36.3 40 PDB header:photosynthesis Chain: 3: PDB Molecule:lhca3; PDBTitle: improved model of plant photosystem i 7 c2o011_ 35.0 44 PDB header:photosynthesis Chain: 1: PDB Molecule:at3g54890; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 8 c2o014_ 34.4 29 PDB header:photosynthesis Chain: 4: PDB Molecule:psi light-harvesting antenna chlorophyll a/b- PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 9 c2o012_ 31.9 21 PDB header:photosynthesis Chain: 2: PDB Molecule:type ii chlorophyll a/b binding protein from PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 10 c3brvB_ 31.3 38 PDB header:transferase/transcription Chain: B: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo/ikkb association domain structure 11 c1afoB_ 31.2 40 PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures 12 c2o013_ 24.1 44 PDB header:photosynthesis Chain: 3: PDB Molecule:psi type iii chlorophyll a/b-binding protein; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 13 c2wsc1_ 19.9 44 PDB header:photosynthesis Chain: 1: PDB Molecule:at3g54890; PDBTitle: improved model of plant photosystem i 14 c2q7cC_ 12.7 64 PDB header:viral protein Chain: C: PDB Molecule:fusion protein between yeast variant gcn4 and PDBTitle: crystal structure of iqn17 15 c2h3oA_ 8.4 42 PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices 16 c1wazA_ 8.1 42 PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles 17 c2vxoB_ 7.5 83 PDB header:ligase Chain: B: PDB Molecule:gmp synthase [glutamine-hydrolyzing]; PDBTitle: human gmp synthetase in complex with xmp 18 c3cyoA_ 6.6 75 PDB header:viral protein Chain: A: PDB Molecule:transmembrane protein; PDBTitle: structure of a longer thermalstable core domain of hiv-12 gp41 containing the enfuvirtide resistance mutation n43d3 and complementary mutation e137k 19 c3o3zA_ 5.7 75 PDB header:viral protein Chain: A: PDB Molecule:envelope glycoprotein gp160; PDBTitle: complex of a chimeric alpha/beta-peptide based on the gp41 chr domain2 bound to a gp41 nhr domain peptide 20 c3uowB_ 5.7 83 PDB header:ligase Chain: B: PDB Molecule:gmp synthetase; PDBTitle: crystal structure of pf10_0123, a gmp synthetase from plasmodium2 falciparum 21 d1h41a2 not modelled 5.3 56 Fold:Zincin-like Superfamily:beta-N-acetylhexosaminidase-like domain Family:alpha-D-glucuronidase, N-terminal 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