Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	S	R	S	D	L	L	T	L	L	T	I	N	F	I	V	V	T	K	G	A	E	R	I	S	E	V	S	A	R	F	T	L	D	A	M	P	G	K	Q	M	A	I	D	A	D	L	N	A	G	L	I	N	Q	A	Q	A	Q	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																														?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	R	K	D	V	A	S	E	A	D	F	Y	G	A	M	D	G	A	S	K	F	V	R	G	D	A	I	A	G	M	M	I	L	A	I	N	L	I	G	G	V	C	I	G	I	F	K	Y	N	L	S	A	D	A	A	F	Q	Q	Y	V
Secondary structure
SS confidence
Disorder														?	?																																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	M	T	I	G	D	G	L	V	A	Q	I	P	S	L	L	L	S	T	A	A	A	I	I	V	T	R	V	S	D	N	G	D	I	A	H	D	V	R	N	Q	L	L	A	S	P	S	V	L	Y	T	A	T	G	I	M	F	V	L	A
Secondary structure
SS confidence
Disorder																															?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	V	P	G	M	P	H	L	P	F	L	L	F	S	A	L	L	G	F	T	G	W	R	M	S	K	Q	P	L	A	A	E	A	E	E	K	S	L	E	T	L	T	R	T	I	T	E	T	S	E	Q	Q	V	S	W	E	T	I	P	L
Secondary structure
SS confidence
Disorder																											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	E	P	I	S	L	S	L	G	Y	K	L	V	A	L	V	D	K	A	Q	G	N	P	L	T	Q	R	I	R	G	V	R	Q	V	I	S	D	G	N	G	V	L	L	P	E	I	R	I	R	E	N	F	R	L	K	P	S	Q	Y	A
Secondary structure
SS confidence
Disorder		?	?										?			?				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	F	I	N	G	I	K	A	D	E	A	D	I	P	A	D	K	L	M	A	L	P	S	S	E	T	Y	G	E	I	D	G	V	Q	G	N	D	P	A	Y	G	M	P	V	T	W	I	Q	A	A	Q	K	A	K	A	L	N	M	G	Y
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		Q	V	I	D	S	A	S	V	I	A	T	H	V	N	K	I	V	R	S	Y	I	P	D	L	F	N	Y	D	D	I	T	Q	L	H	N	R	L	S	S	T	A	P	R	L	A	E	D	L	S	A	A	L	N	Y	S	Q	L	L	K	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		Y	R	A	L	L	T	E	G	V	S	L	R	D	I	V	T	I	A	T	V	L	V	A	S	S	T	V	T	K	D	H	I	L	L	A	A	D	V	R	L	A	L	R	R	S	I	T	H	P	F	V	R	K	Q	E	L	T	V	Y	T
Secondary structure
SS confidence
Disorder																										?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		L	N	N	E	L	E	N	L	L	T	N	V	V	N	Q	A	Q	Q	G	G	K	V	M	L	D	S	V	P	V	D	P	N	M	L	N	Q	F	Q	S	T	M	P	Q	V	K	E	Q	M	K	A	A	G	K	D	P	V	L	L	V	P
Secondary structure
SS confidence
Disorder																?	?	?	?	?	?	?		?	?	?	?	?	?	?	?																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.
Sequence		P	Q	L	R	P	L	L	A	R	Y	A	R	L	F	A	P	G	L	H	V	L	S	Y	N	E	V	P	D	E	L	E	L	K	I	M	G	A	L	M
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 3a5i chain B Region: 229 - 578 Aligned: 340 Modelled: 350 Confidence: 100.0% Identity: 32% PDB header:protein transport Chain: B: PDB Molecule:flagellar biosynthesis protein flha; PDBTitle: structure of the cytoplasmic domain of flha Phyre2 PDB 3myd chain A Region: 231 - 578 Aligned: 342 Modelled: 348 Confidence: 100.0% Identity: 31% PDB header:protein transport Chain: A: PDB Molecule:flagellar biosynthesis protein flha; PDBTitle: structure of the cytoplasmic domain of flha from helicobacter pylori Phyre2 PDB 2x49 chain A Region: 236 - 578 Aligned: 332 Modelled: 343 Confidence: 100.0% Identity: 20% PDB header:protein transport Chain: A: PDB Molecule:invasion protein inva; PDBTitle: crystal structure of the c-terminal domain of inva Phyre2 PDB 3mix chain A Region: 221 - 578 Aligned: 307 Modelled: 318 Confidence: 100.0% Identity: 31% PDB header:protein transport Chain: A: PDB Molecule:flagellar biosynthesis protein flha; PDBTitle: crystal structure of the cytosolic domain of b. subtilis flha Phyre2 PDB 3lw9 chain B Region: 243 - 413 Aligned: 165 Modelled: 171 Confidence: 100.0% Identity: 16% PDB header:protein transport Chain: B: PDB Molecule:invasion protein inva; PDBTitle: structure of a cytoplasmic domain of salmonella inva Phyre2 PDB 3pl4 chain A Region: 379 - 521 Aligned: 125 Modelled: 130 Confidence: 53.7% Identity: 10% PDB header:motor protein Chain: A: PDB Molecule:flagellar motor switch protein; PDBTitle: crystal structure of flig (residue 116-343) from h. pylori Phyre2 PDB 1lm5 chain A Region: 26 - 118 Aligned: 93 Modelled: 93 Confidence: 49.0% Identity: 16% Fold: beta-hairpin-alpha-hairpin repeat Superfamily: Plakin repeat Family: Plakin repeat Phyre2 PDB 2job chain A Region: 48 - 60 Aligned: 13 Modelled: 13 Confidence: 41.8% Identity: 38% PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site Phyre2 PDB 1wi9 chain A Region: 12 - 82 Aligned: 51 Modelled: 52 Confidence: 36.8% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PCI domain (PINT motif) Phyre2 PDB 1jhn chain A domain 4 Region: 295 - 350 Aligned: 45 Modelled: 56 Confidence: 35.2% Identity: 11% Fold: Concanavalin A-like lectins/glucanases Superfamily: Concanavalin A-like lectins/glucanases Family: Calnexin/calreticulin Phyre2 PDB 3t6k chain B Region: 362 - 464 Aligned: 103 Modelled: 103 Confidence: 32.8% Identity: 17% PDB header:signaling protein Chain: B: PDB Molecule:response regulator receiver; PDBTitle: crystal structure of a hypothetical response regulator (caur_3799)2 from chloroflexus aurantiacus j-10-fl at 1.86 a resolution Phyre2 PDB 1vj7 chain B Region: 363 - 562 Aligned: 149 Modelled: 155 Confidence: 30.7% Identity: 17% PDB header:hydrolase, transferase Chain: B: PDB Molecule:bifunctional rela/spot; PDBTitle: crystal structure of the bifunctional catalytic fragment of relseq,2 the rela/spot homolog from streptococcus equisimilis. Phyre2 PDB 3mtu chain D Region: 43 - 72 Aligned: 30 Modelled: 30 Confidence: 29.6% Identity: 23% PDB header:contractile protein Chain: D: PDB Molecule:tropomyosin alpha-1 chain, microtubule-associated protein PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle Phyre2 PDB 2f2e chain A domain 1 Region: 379 - 447 Aligned: 67 Modelled: 66 Confidence: 28.1% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: HxlR-like Phyre2 PDB 1pvd chain A domain 1 Region: 502 - 562 Aligned: 55 Modelled: 61 Confidence: 26.6% Identity: 16% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Pyruvate oxidase and decarboxylase, middle domain Phyre2 PDB 2fsw chain A domain 1 Region: 400 - 447 Aligned: 47 Modelled: 46 Confidence: 26.6% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: HxlR-like Phyre2 PDB 3bhw chain A Region: 423 - 492 Aligned: 63 Modelled: 70 Confidence: 26.3% Identity: 10% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from magnetospirillum2 magneticum Phyre2 PDB 1zpd chain A domain 1 Region: 510 - 562 Aligned: 47 Modelled: 51 Confidence: 26.1% Identity: 21% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Pyruvate oxidase and decarboxylase, middle domain Phyre2 PDB 2peo chain A Region: 372 - 428 Aligned: 57 Modelled: 57 Confidence: 24.4% Identity: 19% PDB header:chaperone Chain: A: PDB Molecule:rbcx protein; PDBTitle: crystal structure of rbcx from anabaena ca Phyre2 PDB 2peo chain A domain 1 Region: 372 - 428 Aligned: 57 Modelled: 57 Confidence: 24.4% Identity: 19% Fold: RbcX-like Superfamily: RbcX-like Family: RbcX-like Phyre2 1 c3a5iB_ 2 c3mydA_ 3 c2x49A_ 4 c3mixA_ 5 c3lw9B_ 6 c3pl4A_ 7 d1lm5a_ 8 c2jobA_ 9 d1wi9a_ 10 d1jhna4 11 c3t6kB_ 12 c1vj7B_ 13 c3mtuD_ 14 d2f2ea1 15 d1pvda1 16 d2fswa1 17 c3bhwA_ 18 d1zpda1 19 c2peoA_ 20 d2peoa1 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 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99

Detailed template information

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

1 c3a5iB_ 100.0 32 PDB header:protein transport Chain: B: PDB Molecule:flagellar biosynthesis protein flha; PDBTitle: structure of the cytoplasmic domain of flha 2 c3mydA_ 100.0 31 PDB header:protein transport Chain: A: PDB Molecule:flagellar biosynthesis protein flha; PDBTitle: structure of the cytoplasmic domain of flha from helicobacter pylori 3 c2x49A_ 100.0 20 PDB header:protein transport Chain: A: PDB Molecule:invasion protein inva; PDBTitle: crystal structure of the c-terminal domain of inva 4 c3mixA_ 100.0 31 PDB header:protein transport Chain: A: PDB Molecule:flagellar biosynthesis protein flha; PDBTitle: crystal structure of the cytosolic domain of b. subtilis flha 5 c3lw9B_ 100.0 16 PDB header:protein transport Chain: B: PDB Molecule:invasion protein inva; PDBTitle: structure of a cytoplasmic domain of salmonella inva 6 c3pl4A_ 53.7 10 PDB header:motor protein Chain: A: PDB Molecule:flagellar motor switch protein; PDBTitle: crystal structure of flig (residue 116-343) from h. pylori 7 d1lm5a_ 49.0 16 Fold:beta-hairpin-alpha-hairpin repeat Superfamily:Plakin repeat Family:Plakin repeat 8 c2jobA_ 41.8 38 PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site 9 d1wi9a_ 36.8 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PCI domain (PINT motif) 10 d1jhna4 35.2 11 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Calnexin/calreticulin 11 c3t6kB_ 32.8 17 PDB header:signaling protein Chain: B: PDB Molecule:response regulator receiver; PDBTitle: crystal structure of a hypothetical response regulator (caur_3799)2 from chloroflexus aurantiacus j-10-fl at 1.86 a resolution 12 c1vj7B_ 30.7 17 PDB header:hydrolase, transferase Chain: B: PDB Molecule:bifunctional rela/spot; PDBTitle: crystal structure of the bifunctional catalytic fragment of relseq,2 the rela/spot homolog from streptococcus equisimilis. 13 c3mtuD_ 29.6 23 PDB header:contractile protein Chain: D: PDB Molecule:tropomyosin alpha-1 chain, microtubule-associated protein PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle 14 d2f2ea1 28.1 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:HxlR-like 15 d1pvda1 26.6 16 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain 16 d2fswa1 26.6 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:HxlR-like 17 c3bhwA_ 26.3 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from magnetospirillum2 magneticum 18 d1zpda1 26.1 21 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain 19 c2peoA_ 24.4 19 PDB header:chaperone Chain: A: PDB Molecule:rbcx protein; PDBTitle: crystal structure of rbcx from anabaena ca 20 d2peoa1 24.4 19 Fold:RbcX-like Superfamily:RbcX-like Family:RbcX-like 21 c4a5mH_ not modelled 24.2 14 PDB header:transcription Chain: H: PDB Molecule:uncharacterized hth-type transcriptional regulator yybr; PDBTitle: redox regulator hypr in its oxidized form 22 c3hjlA_ not modelled 23.9 15 PDB header:proton transport Chain: A: PDB Molecule:flagellar motor switch protein flig; PDBTitle: the structure of full-length flig from aquifex aeolicus 23 c2o2fA_ not modelled 23.8 12 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: solution structure of the anti-apoptotic protein bcl-2 in2 complex with an acyl-sulfonamide-based ligand 24 c2lkyA_ not modelled 23.5 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of msmeg_1053, the second duf3349 annotated protein2 in the genome of mycobacterium smegmatis, seattle structural genomics3 center for infectious disease target mysma.17112.b 25 c2q2kA_ not modelled 22.8 41 PDB header:dna binding protein/dna Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of nucleic-acid binding protein 26 c3pihA_ not modelled 22.1 14 PDB header:hydrolase/dna Chain: A: PDB Molecule:uvrabc system protein a; PDBTitle: t. maritima uvra in complex with fluorescein-modified dna 27 c3rg0A_ not modelled 21.0 17 PDB header:chaperone Chain: A: PDB Molecule:calreticulin; PDBTitle: structural and functional relationships between the lectin and arm2 domains of calreticulin 28 c2kvcA_ not modelled 20.6 19 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: solution structure of the mycobacterium tuberculosis protein rv0543c,2 a member of the duf3349 superfamily. seattle structural genomics3 center for infectious disease target mytud.17112.a 29 c3kmgE_ not modelled 20.0 28 PDB header:transcription Chain: E: PDB Molecule:steroid receptor coactivator-1; PDBTitle: the x-ray crystal structure of ppar-gamma in complex with an indole2 derivative modulator, gsk538, and an src-1 peptide 30 d1orna_ not modelled 19.9 12 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:Endonuclease III 31 c1t98B_ not modelled 19.7 20 PDB header:cell cycle Chain: B: PDB Molecule:chromosome partition protein mukf; PDBTitle: crystal structure of mukf(1-287) 32 c1zcjA_ not modelled 19.4 12 PDB header:oxidoreductase Chain: A: PDB Molecule:peroxisomal bifunctional enzyme; PDBTitle: crystal structure of 3-hydroxyacyl-coa dehydrogenase 33 c1t6sB_ not modelled 19.2 11 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of a conserved hypothetical protein from chlorobium2 tepidum 34 c3pkrA_ not modelled 19.0 10 PDB header:motor protein Chain: A: PDB Molecule:flagellar motor switch protein; PDBTitle: crystal structure of flig (residue 86-343) from h. pylori 35 c1b35D_ not modelled 17.2 22 PDB header:virus Chain: D: PDB Molecule:protein (cricket paralysis virus, vp4); PDBTitle: cricket paralysis virus (crpv) 36 d1qhma_ not modelled 16.7 44 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like 37 c2z99A_ not modelled 15.3 9 PDB header:cell cycle Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of scpb from mycobacterium tuberculosis 38 d2h9fa2 not modelled 15.3 18 Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PA0793-like 39 c3a11D_ not modelled 15.0 9 PDB header:isomerase Chain: D: PDB Molecule:translation initiation factor eif-2b, delta PDBTitle: crystal structure of ribose-1,5-bisphosphate isomerase from2 thermococcus kodakaraensis kod1 40 c2hfpB_ not modelled 14.9 38 PDB header:transcription Chain: B: PDB Molecule:src peptide fragment; PDBTitle: crystal structure of ppar gamma with n-sulfonyl-2-indole2 carboxamide ligands 41 c3cfyA_ not modelled 14.9 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative luxo repressor protein; PDBTitle: crystal structure of signal receiver domain of putative luxo2 repressor protein from vibrio parahaemolyticus 42 d1ovma1 not modelled 14.8 14 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain 43 c2cdqB_ not modelled 14.8 8 PDB header:transferase Chain: B: PDB Molecule:aspartokinase; PDBTitle: crystal structure of arabidopsis thaliana aspartate kinase2 complexed with lysine and s-adenosylmethionine 44 c3df8A_ not modelled 14.7 13 PDB header:transcription Chain: A: PDB Molecule:possible hxlr family transcriptional factor; PDBTitle: the crystal structure of a possible hxlr family transcriptional factor2 from thermoplasma volcanium gss1 45 c1k74E_ not modelled 14.7 38 PDB header:transcription Chain: E: PDB Molecule:steroid receptor coactivator; PDBTitle: the 2.3 angstrom resolution crystal structure of the2 heterodimer of the human ppargamma and rxralpha ligand3 binding domains respectively bound with gw409544 and 9-cis4 retinoic acid and co-activator peptides. 46 c1fm6E_ not modelled 14.7 38 PDB header:transcription Chain: E: PDB Molecule:steroid receptor coactivator; PDBTitle: the 2.1 angstrom resolution crystal structure of the2 heterodimer of the human rxralpha and ppargamma ligand3 binding domains respectively bound with 9-cis retinoic4 acid and rosiglitazone and co-activator peptides. 47 c1fm9E_ not modelled 14.7 38 PDB header:transcription Chain: E: PDB Molecule:steroid receptor coactivator; PDBTitle: the 2.1 angstrom resolution crystal structure of the2 heterodimer of the human rxralpha and ppargamma ligand3 binding domains respectively bound with 9-cis retinoic4 acid and gi262570 and co-activator peptides. 48 c1fm6V_ not modelled 14.4 38 PDB header:transcription Chain: V: PDB Molecule:steroid receptor coactivator; PDBTitle: the 2.1 angstrom resolution crystal structure of the2 heterodimer of the human rxralpha and ppargamma ligand3 binding domains respectively bound with 9-cis retinoic4 acid and rosiglitazone and co-activator peptides. 49 d1wpga4 not modelled 14.3 22 Fold:Calcium ATPase, transmembrane domain M Superfamily:Calcium ATPase, transmembrane domain M Family:Calcium ATPase, transmembrane domain M 50 c3s93B_ not modelled 14.0 16 PDB header:transcription Chain: B: PDB Molecule:tudor domain-containing protein 5; PDBTitle: crystal structure of conserved motif in tdrd5 51 c3m65A_ not modelled 13.8 11 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent protease la 1; PDBTitle: crystal structure of bacillus subtilis lon n-terminal domain 52 d1h16a_ not modelled 13.6 44 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like 53 d1j6ra_ not modelled 12.4 10 Fold:Methionine synthase activation domain-like Superfamily:Methionine synthase activation domain-like Family:Hypothetical protein TM0269 54 c1p8dC_ not modelled 12.2 31 PDB header:membrane protein/protein binding Chain: C: PDB Molecule:nuclear receptor coactivator 1 isoform 3; PDBTitle: x-ray crystal structure of lxr ligand binding domain with 24(s),25-2 epoxycholesterol 55 d1niga_ not modelled 12.2 18 Fold:Ferritin-like Superfamily:Cobalamin adenosyltransferase-like Family:Hypothetical protein Ta1238 56 d1a68a_ not modelled 12.2 25 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 57 c3dnfB_ not modelled 12.1 17 PDB header:oxidoreductase Chain: B: PDB Molecule:4-hydroxy-3-methylbut-2-enyl diphosphate reductase; PDBTitle: structure of (e)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase,2 the terminal enzyme of the non-mevalonate pathway 58 c3ol4B_ not modelled 12.0 14 PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c 59 c2ka1A_ not modelled 12.0 86 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 60 c2ka2B_ not modelled 12.0 86 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 61 c2ka1B_ not modelled 12.0 86 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 62 c2ka2A_ not modelled 12.0 86 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 63 c2oviA_ not modelled 11.7 13 PDB header:ligand binding protein, metal transport Chain: A: PDB Molecule:hypothetical protein chux; PDBTitle: structure of the heme binding protein chux 64 c2prgC_ not modelled 11.5 38 PDB header:complex (thiazolidinedione/receptor) Chain: C: PDB Molecule:nuclear receptor coactivator src-1; PDBTitle: ligand-binding domain of the human peroxisome proliferator2 activated receptor gamma 65 c1cpbA_ not modelled 11.3 24 PDB header:hydrolase (c-terminal peptidase) Chain: A: PDB Molecule:carboxypeptidase b; PDBTitle: structure of carboxypeptidase b at 2.8 angstroms resolution 66 d1wfra_ not modelled 11.1 27 Fold:SCP-like Superfamily:SCP-like Family:Sterol carrier protein, SCP 67 c1nw3A_ not modelled 11.1 23 PDB header:transferase Chain: A: PDB Molecule:histone methyltransferase dot1l; PDBTitle: structure of the catalytic domain of human dot1l, a non-set2 domain nucleosomal histone methyltransferase 68 d1nw3a_ not modelled 11.1 23 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Catalytic, N-terminal domain of histone methyltransferase Dot1l 69 c2q9qF_ not modelled 11.0 12 PDB header:replication Chain: F: PDB Molecule:gins complex subunit 4; PDBTitle: the crystal structure of full length human gins complex 70 d1ugpa_ not modelled 11.0 16 Fold:Nitrile hydratase alpha chain Superfamily:Nitrile hydratase alpha chain Family:Nitrile hydratase alpha chain 71 c3ke8A_ not modelled 10.9 17 PDB header:oxidoreductase Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-enyl diphosphate PDBTitle: crystal structure of isph:hmbpp-complex 72 d1ckqa_ not modelled 10.6 13 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease EcoRI 73 d1zh2a1 not modelled 10.6 16 Fold:Flavodoxin-like Superfamily:CheY-like Family:CheY-related 74 d2a9ha1 not modelled 10.6 19 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 75 d3b60a2 not modelled 10.4 5 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 76 d1r2za1 not modelled 10.3 12 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 77 d1dsxa_ not modelled 10.0 27 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 78 c3gz6A_ not modelled 9.9 15 PDB header:dna binding protein/dna Chain: A: PDB Molecule:mutt/nudix family protein; PDBTitle: crystal structure of shewanella oneidensis nrtr complexed2 with a 27mer dna 79 d2iuba2 not modelled 9.7 17 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 80 c3nvtA_ not modelled 9.5 15 PDB header:transferase/isomerase Chain: A: PDB Molecule:3-deoxy-d-arabino-heptulosonate 7-phosphate synthase; PDBTitle: 1.95 angstrom crystal structure of a bifunctional 3-deoxy-7-2 phosphoheptulonate synthase/chorismate mutase (aroa) from listeria3 monocytogenes egd-e 81 d1r3jc_ not modelled 9.2 17 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 82 d2e9xd1 not modelled 9.0 10 Fold:GINS helical bundle-like Superfamily:GINS helical bundle-like Family:SLD5 N-terminal domain-like 83 c2yujA_ not modelled 8.9 27 PDB header:protein binding Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like; PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1 84 c2rmrA_ not modelled 8.9 11 PDB header:transcription Chain: A: PDB Molecule:paired amphipathic helix protein sin3a; PDBTitle: solution structure of msin3a pah1 domain 85 c2f3oB_ not modelled 8.8 31 PDB header:unknown function Chain: B: PDB Molecule:pyruvate formate-lyase 2; PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus 86 d1jm6a1 not modelled 8.7 7 Fold:Bromodomain-like Superfamily:alpha-ketoacid dehydrogenase kinase, N-terminal domain Family:alpha-ketoacid dehydrogenase kinase, N-terminal domain 87 c1p8dD_ not modelled 8.7 45 PDB header:membrane protein/protein binding Chain: D: PDB Molecule:nuclear receptor coactivator 1 isoform 3; PDBTitle: x-ray crystal structure of lxr ligand binding domain with 24(s),25-2 epoxycholesterol 88 c2bbjB_ not modelled 8.7 20 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 89 c1j8yF_ not modelled 8.6 10 PDB header:signaling protein Chain: F: PDB Molecule:signal recognition 54 kda protein; PDBTitle: signal recognition particle conserved gtpase domain from a.2 ambivalens t112a mutant 90 c3d4uA_ not modelled 8.5 13 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:carboxypeptidase b2; PDBTitle: bovine thrombin-activatable fibrinolysis inhibitor (tafia) in complex2 with tick-derived carboxypeptidase inhibitor. 91 c1mhsA_ not modelled 8.4 17 PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase 92 c2ejaB_ not modelled 8.4 11 PDB header:lyase Chain: B: PDB Molecule:uroporphyrinogen decarboxylase; PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 aquifex aeolicus 93 d1b0na1 not modelled 8.4 25 Fold:Dimerisation interlock Superfamily:SinR repressor dimerisation domain-like Family:SinR repressor dimerisation domain-like 94 c2k1oA_ not modelled 8.3 21 PDB header:gene regulation Chain: A: PDB Molecule:putative; PDBTitle: nmr structure of helicobacter pylori jhp0511 (hp0564). 95 c1zc1A_ not modelled 8.2 13 PDB header:protein turnover Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1; PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites 96 c3k5wA_ not modelled 8.2 21 PDB header:transferase Chain: A: PDB Molecule:carbohydrate kinase; PDBTitle: crystal structure of a carbohydrate kinase (yjef family)from2 helicobacter pylori 97 c4ktqA_ not modelled 8.2 15 PDB header:transferase/dna Chain: A: PDB Molecule:protein (large fragment of dna polymerase i); PDBTitle: binary complex of the large fragment of dna polymerase i2 from t. aquaticus bound to a primer/template dna 98 d1lvaa3 not modelled 8.0 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal fragment of elongation factor SelB 99 d1iuka_ not modelled 7.9 16 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:CoA-binding 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