Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	F	K	Q	Y	L	Q	V	T	K	P	G	I	I	F	G	N	L	I	S	V	I	G	G	F	L	L	A	S	K	G	S	I	D	Y	P	L	F	I	Y	T	L	V	G	V	S	L	V	V	A	S	G	C	V	F	N	N	Y	I
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	R	D	I	D	R	K	M	E	R	T	K	N	R	V	L	V	K	G	L	I	S	P	A	V	S	L	V	Y	A	T	L	L	G	I	A	G	F	M	L	L	W	F	G	A	N	P	L	A	C	W	L	G	V	M	G	F	V	V	Y
Secondary structure
SS confidence
Disorder																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	G	V	Y	S	L	Y	M	K	R	H	S	V	Y	G	T	L	I	G	S	L	S	G	A	A	P	P	V	I	G	Y	C	A	V	T	G	E	F	D	S	G	A	A	I	L	L	A	I	F	S	L	W	Q	M	P	H	S	Y	A	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	I	F	R	F	K	D	Y	Q	A	A	N	I	P	V	L	P	V	V	K	G	I	S	V	A	K	N	H	I	T	L	Y	I	I	A	F	A	V	A	T	L	M	L	S	L	G	G	Y	A	G	Y	K	Y	L	V	V	A	A	A	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.
Sequence		S	V	W	W	L	G	M	A	L	R	G	Y	K	V	A	D	D	R	I	W	A	R	K	L	F	G	F	S	I	I	A	I	T	A	L	S	V	M	M	S	V	D	F	M	V	P	D	S	H	T	L	L	A	A	V	W
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 3m9u chain D Region: 22 - 213 Aligned: 189 Modelled: 189 Confidence: 94.9% Identity: 12% PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 Phyre2 PDB 3ts7 chain B Region: 10 - 213 Aligned: 191 Modelled: 201 Confidence: 94.4% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus Phyre2 PDB 3lsn chain A Region: 42 - 213 Aligned: 168 Modelled: 169 Confidence: 87.8% Identity: 17% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of putative geranyltranstransferase from pseudomonas2 fluorescens pf-5 complexed with magnesium Phyre2 PDB 1v4e chain A Region: 1 - 89 Aligned: 83 Modelled: 89 Confidence: 87.8% Identity: 14% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 1rqj chain A Region: 10 - 213 Aligned: 190 Modelled: 201 Confidence: 83.1% Identity: 13% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 2o1o chain B Region: 18 - 200 Aligned: 178 Modelled: 183 Confidence: 71.1% Identity: 12% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative farnesyl pyrophosphate synthase; PDBTitle: cryptosporidium parvum putative polyprenyl pyrophosphate2 synthase (cgd4_2550) in complex with risedronate. Phyre2 PDB 1yhl chain A Region: 1 - 89 Aligned: 87 Modelled: 89 Confidence: 71.0% Identity: 11% PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: structure of the complex of trypanosoma cruzi farnesyl diphosphate2 synthase with risedronate, dmapp and mg+2 Phyre2 PDB 2f94 chain F Region: 1 - 89 Aligned: 87 Modelled: 89 Confidence: 64.2% Identity: 13% PDB header:transferase Chain: F: PDB Molecule:farnesyl diphosphate synthase; PDBTitle: crystal structure of human fpps in complex with ibandronate Phyre2 PDB 3aq0 chain G Region: 1 - 89 Aligned: 86 Modelled: 89 Confidence: 62.7% Identity: 9% PDB header:transferase Chain: G: PDB Molecule:geranyl diphosphate synthase; PDBTitle: ligand-bound form of arabidopsis medium/long-chain length prenyl2 pyrophosphate synthase (surface polar residue mutant) Phyre2 PDB 3tc1 chain A Region: 1 - 89 Aligned: 83 Modelled: 89 Confidence: 61.1% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:octaprenyl pyrophosphate synthase; PDBTitle: crystal structure of octaprenyl pyrophosphate synthase from2 helicobacter pylori Phyre2 PDB 3cp6 chain A Region: 2 - 89 Aligned: 86 Modelled: 88 Confidence: 60.7% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthetase; PDBTitle: crystal structure of human farnesyl diphosphate synthase (t201a2 mutant) complexed with mg and biphosphonate inhibitor Phyre2 PDB 1fps chain A Region: 1 - 89 Aligned: 87 Modelled: 89 Confidence: 56.2% Identity: 11% Fold: Terpenoid synthases Superfamily: Terpenoid synthases Family: Isoprenyl diphosphate synthases Phyre2 PDB 3ez3 chain A Region: 2 - 89 Aligned: 87 Modelled: 88 Confidence: 55.3% Identity: 10% PDB header:lyase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase, putative; PDBTitle: crystal structure of plasmodium vivax geranylgeranylpyrophosphate2 synthase pvx_092040 with zoledronate and ipp bound Phyre2 PDB 3kra chain B Region: 142 - 217 Aligned: 75 Modelled: 76 Confidence: 52.4% Identity: 12% PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small subunit; PDBTitle: mint heterotetrameric geranyl pyrophosphate synthase in2 complex with magnesium Phyre2 PDB 1wmw chain A Region: 1 - 89 Aligned: 85 Modelled: 89 Confidence: 52.3% Identity: 7% PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl diphosphate synthetase; PDBTitle: crystal structure of geranulgeranyl diphosphate synthase from thermus2 thermophilus Phyre2 PDB 3p8r chain A Region: 1 - 68 Aligned: 66 Modelled: 68 Confidence: 52.0% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of polyprenyl synthase from vibrio cholerae Phyre2 PDB 3mzv chain B Region: 22 - 200 Aligned: 173 Modelled: 179 Confidence: 50.7% Identity: 16% PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus Phyre2 PDB 3nf2 chain A Region: 2 - 89 Aligned: 85 Modelled: 88 Confidence: 48.3% Identity: 9% PDB header:transferase Chain: A: PDB Molecule:putative polyprenyl synthetase; PDBTitle: crystal structure of polyprenyl synthetase from streptomyces2 coelicolor a3(2) Phyre2 PDB 2ogd chain B Region: 1 - 89 Aligned: 87 Modelled: 89 Confidence: 47.8% Identity: 11% PDB header:transferase Chain: B: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: t. brucei farnesyl diphosphate synthase complexed with bisphosphonate2 bph-527 Phyre2 PDB 3rmg chain B Region: 1 - 89 Aligned: 84 Modelled: 89 Confidence: 47.5% Identity: 7% PDB header:transferase Chain: B: PDB Molecule:octaprenyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase from2 bacteroides thetaiotaomicron Phyre2 1 c3m9uD_ 2 c3ts7B_ 3 c3lsnA_ 4 d1v4ea_ 5 d1rqja_ 6 c2o1oB_ 7 c1yhlA_ 8 c2f94F_ 9 c3aq0G_ 10 c3tc1A_ 11 c3cp6A_ 12 d1fpsa_ 13 c3ez3A_ 14 c3kraB_ 15 c1wmwA_ 16 c3p8rA_ 17 c3mzvB_ 18 c3nf2A_ 19 c2ogdB_ 20 c3rmgB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52

Detailed template information

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

1 c3m9uD_ 94.9 12 PDB header:transferase Chain: D: PDB Molecule:farnesyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from lactobacillus brevis atcc 367 2 c3ts7B_ 94.4 13 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of farnesyl diphosphate synthase (target efi-501951)2 from methylococcus capsulatus 3 c3lsnA_ 87.8 17 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of putative geranyltranstransferase from pseudomonas2 fluorescens pf-5 complexed with magnesium 4 d1v4ea_ 87.8 14 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 5 d1rqja_ 83.1 13 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 6 c2o1oB_ 71.1 12 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative farnesyl pyrophosphate synthase; PDBTitle: cryptosporidium parvum putative polyprenyl pyrophosphate2 synthase (cgd4_2550) in complex with risedronate. 7 c1yhlA_ 71.0 11 PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: structure of the complex of trypanosoma cruzi farnesyl diphosphate2 synthase with risedronate, dmapp and mg+2 8 c2f94F_ 64.2 13 PDB header:transferase Chain: F: PDB Molecule:farnesyl diphosphate synthase; PDBTitle: crystal structure of human fpps in complex with ibandronate 9 c3aq0G_ 62.7 9 PDB header:transferase Chain: G: PDB Molecule:geranyl diphosphate synthase; PDBTitle: ligand-bound form of arabidopsis medium/long-chain length prenyl2 pyrophosphate synthase (surface polar residue mutant) 10 c3tc1A_ 61.1 16 PDB header:transferase Chain: A: PDB Molecule:octaprenyl pyrophosphate synthase; PDBTitle: crystal structure of octaprenyl pyrophosphate synthase from2 helicobacter pylori 11 c3cp6A_ 60.7 13 PDB header:transferase Chain: A: PDB Molecule:farnesyl pyrophosphate synthetase; PDBTitle: crystal structure of human farnesyl diphosphate synthase (t201a2 mutant) complexed with mg and biphosphonate inhibitor 12 d1fpsa_ 56.2 11 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 13 c3ez3A_ 55.3 10 PDB header:lyase Chain: A: PDB Molecule:farnesyl pyrophosphate synthase, putative; PDBTitle: crystal structure of plasmodium vivax geranylgeranylpyrophosphate2 synthase pvx_092040 with zoledronate and ipp bound 14 c3kraB_ 52.4 12 PDB header:transferase Chain: B: PDB Molecule:geranyl diphosphate synthase small subunit; PDBTitle: mint heterotetrameric geranyl pyrophosphate synthase in2 complex with magnesium 15 c1wmwA_ 52.3 7 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl diphosphate synthetase; PDBTitle: crystal structure of geranulgeranyl diphosphate synthase from thermus2 thermophilus 16 c3p8rA_ 52.0 12 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of polyprenyl synthase from vibrio cholerae 17 c3mzvB_ 50.7 16 PDB header:transferase Chain: B: PDB Molecule:decaprenyl diphosphate synthase; PDBTitle: crystal structure of a decaprenyl diphosphate synthase from2 rhodobacter capsulatus 18 c3nf2A_ 48.3 9 PDB header:transferase Chain: A: PDB Molecule:putative polyprenyl synthetase; PDBTitle: crystal structure of polyprenyl synthetase from streptomyces2 coelicolor a3(2) 19 c2ogdB_ 47.8 11 PDB header:transferase Chain: B: PDB Molecule:farnesyl pyrophosphate synthase; PDBTitle: t. brucei farnesyl diphosphate synthase complexed with bisphosphonate2 bph-527 20 c3rmgB_ 47.5 7 PDB header:transferase Chain: B: PDB Molecule:octaprenyl-diphosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase from2 bacteroides thetaiotaomicron 21 d2q80a1 not modelled 46.6 8 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Isoprenyl diphosphate synthases 22 c3n3dB_ not modelled 45.9 14 PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase from2 lactobacillus brevis atcc 367 23 c2j1pB_ not modelled 44.3 11 PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba in2 complex with ggpp 24 c3llwA_ not modelled 36.4 11 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase (ispa); PDBTitle: crystal structure of geranyltransferase from helicobacter2 pylori 26695 25 c3p8lB_ not modelled 33.4 11 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of polyprenyl synthase from enterococcus faecalis2 v583 26 c3lmdA_ not modelled 31.8 12 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthase2 from corynebacterium glutamicum atcc 13032 27 c2e8xB_ not modelled 28.7 11 PDB header:transferase Chain: B: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: s. cerevisiae geranylgeranyl pyrophosphate synthase in2 complex with magnesium and gpp 28 c3dh4A_ not modelled 23.6 11 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 29 c2j1oA_ not modelled 23.0 11 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: geranylgeranyl diphosphate synthase from sinapis alba 30 c2xq2A_ not modelled 19.5 11 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 31 c1wy0A_ not modelled 16.2 16 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthetase; PDBTitle: crystal structure of geranylgeranyl pyrophosphate synthetase from2 pyrococcus horikoshii ot3 32 c3aqbD_ not modelled 15.1 12 PDB header:transferase Chain: D: PDB Molecule:component b of hexaprenyl diphosphate synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium 33 d1qlec_ not modelled 14.8 10 Fold:Cytochrome c oxidase subunit III-like Superfamily:Cytochrome c oxidase subunit III-like Family:Cytochrome c oxidase subunit III-like 34 c2ftzA_ not modelled 14.1 7 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of geranyltranstransferase (ec 2.5.1.10) (tm0161)2 from thermotoga maritima at 1.90 a resolution 35 d1m9dc_ not modelled 13.1 15 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 36 d1diha2 not modelled 12.5 18 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like 37 c3oyrB_ not modelled 11.5 16 PDB header:transferase Chain: B: PDB Molecule:trans-isoprenyl diphosphate synthase; PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate 38 c1l6nA_ not modelled 10.4 12 PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal 283-residue fragment of the hiv-2 1 gag polyprotein 39 d1m9fd_ not modelled 9.6 12 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 40 c2h8oA_ not modelled 8.8 15 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: the 1.6a crystal structure of the geranyltransferase from2 agrobacterium tumefaciens 41 c2forB_ not modelled 7.7 12 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of the shigella flexneri farnesyl pyrophosphate2 synthase complex with an isopentenyl pyrophosphate 42 c2wlvA_ not modelled 6.9 10 PDB header:virus protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal capsid domain of hiv-2 43 d2pxrc1 not modelled 6.8 12 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 44 c2zcpA_ not modelled 6.7 0 PDB header:transferase Chain: A: PDB Molecule:dehydrosqualene synthase; PDBTitle: crystal structure of the c(30) carotenoid dehydrosqualene2 synthase from staphylococcus aureus complexed with3 farnesyl thiopyrophosphate 45 c3lk5A_ not modelled 6.6 10 PDB header:transferase Chain: A: PDB Molecule:geranylgeranyl pyrophosphate synthase; PDBTitle: crystal structure of putative geranylgeranyl pyrophosphate synthase2 from corynebacterium glutamicum 46 d1ezfa_ not modelled 6.5 12 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Squalene synthase 47 c3lomA_ not modelled 6.4 9 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of geranyltransferase from legionella2 pneumophila 48 c3oyrA_ not modelled 6.2 10 PDB header:transferase Chain: A: PDB Molecule:trans-isoprenyl diphosphate synthase; PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate 49 c3am6C_ not modelled 5.8 9 PDB header:transport protein Chain: C: PDB Molecule:rhodopsin-2; PDBTitle: crystal structure of the proton pumping rhodopsin ar2 from marine alga2 acetabularia acetabulum 50 c3ipiA_ not modelled 5.3 15 PDB header:transferase Chain: A: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of a geranyltranstransferase from the2 methanosarcina mazei 51 d1te7a_ not modelled 5.1 22 Fold:PUA domain-like Superfamily:PUA domain-like Family:yqfB-like 52 c3ucaB_ not modelled 5.1 11 PDB header:transferase Chain: B: PDB Molecule:geranyltranstransferase; PDBTitle: crystal structure of isoprenoid synthase (target efi-501974) from2 clostridium perfringens

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