Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	L	L	Q	F	S	G	L	F	V	V	W	L	L	C	T	L	F	I	A	T	L	T	W	F	E	F	R	R	V	R	F	N	F	N	V	F	F	S	L	L	F	L	L	T	F	F	F	G	F	P	L	T	S	V	L	V	F	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	D	V	G	V	A	P	P	E	I	L	L	Q	A	L	L	S	A	G	C	F	Y	A	V	Y	Y	V	T	Y	K	T	R	L	R	K	R	V	A	D	V	P	R	R	P	L	F	T	M	N	R	V	E	T	N	L	T	W	V	I	L
Secondary structure
SS confidence
Disorder																																																		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	G	I	A	L	V	S	V	G	I	F	F	M	H	N	G	F	L	L	F	R	L	N	S	Y	S	Q	I	F	S	S	E	V	S	G	V	A	L	K	R	F	F	Y	F	F	I	P	A	M	L	V	V	Y	F	L	R	Q	D	S	K
Secondary structure
SS confidence
Disorder																																	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	W	L	F	F	L	V	S	T	V	A	F	G	L	L	T	Y	M	I	V	G	G	T	R	A	N	I	I	I	A	F	A	I	F	L	F	I	G	I	I	R	G	W	I	S	L	W	M	L	A	A	A	G	V	L	G	I	V	G	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	W	L	A	L	K	R	Y	G	M	N	V	S	G	D	E	A	F	Y	T	F	L	Y	L	T	R	D	T	F	S	P	W	E	N	L	A	L	L	L	Q	N	Y	D	N	I	D	F	Q	G	L	A	P	I	V	R	D	F	Y	V	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	P	S	W	L	W	P	G	R	P	S	M	V	L	N	S	A	N	Y	F	T	W	E	V	L	N	N	H	S	G	L	A	I	S	P	T	L	I	G	S	L	V	V	M	G	G	A	L	F	I	P	L	G	A	I	V	V	G	L	I
Secondary structure
SS confidence
Disorder																														?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		I	K	W	F	D	W	L	Y	E	L	G	N	R	E	P	N	R	Y	K	A	A	I	L	H	S	F	C	F	G	A	I	F	N	M	I	V	L	A	R	E	G	L	D	S	F	V	S	R	V	V	F	F	I	V	V	F	G	A	C	L
Secondary structure
SS confidence
Disorder													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450
Sequence		M	I	A	K	L	L	Y	W	L	F	E	S	A	G	L	I	H	K	R	T	K	S	S	L	R	T	Q	V	E	G
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 2pid chain B Region: 266 - 319 Aligned: 53 Modelled: 54 Confidence: 15.3% Identity: 17% PDB header:ligase Chain: B: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of human mitochondrial tyrosyl-trna synthetase in2 complex with an adenylate analog Phyre2 PDB 2wwa chain C Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 13.4% Identity: 38% PDB header:ribosome Chain: C: PDB Molecule:protein transport protein seb2; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 3ipd chain B Region: 176 - 202 Aligned: 27 Modelled: 27 Confidence: 12.2% Identity: 15% PDB header:exocytosis Chain: B: PDB Molecule:syntaxin-1a; PDBTitle: helical extension of the neuronal snare complex into the2 membrane, spacegroup i 21 21 21 Phyre2 PDB 2vqz chain B Region: 237 - 290 Aligned: 49 Modelled: 54 Confidence: 11.8% Identity: 22% PDB header:transcription Chain: B: PDB Molecule:polymerase basic protein 2; PDBTitle: structure of the cap-binding domain of influenza virus2 polymerase subunit pb2 with bound m7gtp Phyre2 PDB 2l9u chain A Region: 329 - 353 Aligned: 25 Modelled: 25 Confidence: 10.9% Identity: 44% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain Phyre2 PDB 2axt chain J domain 1 Region: 228 - 242 Aligned: 15 Modelled: 15 Confidence: 10.6% Identity: 47% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 PDB 3d9w chain A Region: 390 - 434 Aligned: 30 Modelled: 30 Confidence: 10.2% Identity: 30% PDB header:transferase Chain: A: PDB Molecule:putative acetyltransferase; PDBTitle: crystal structure analysis of nocardia farcinica arylamine2 n-acetyltransferase Phyre2 PDB 1qf8 chain A Region: 423 - 439 Aligned: 11 Modelled: 17 Confidence: 8.8% Identity: 73% Fold: Rubredoxin-like Superfamily: Casein kinase II beta subunit Family: Casein kinase II beta subunit Phyre2 PDB 3dvj chain B Region: 167 - 181 Aligned: 15 Modelled: 15 Confidence: 8.7% Identity: 20% PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain (without cloning2 artifact, hm to tv) complex Phyre2 PDB 1jb3 chain A Region: 302 - 317 Aligned: 16 Modelled: 16 Confidence: 8.5% Identity: 44% Fold: OB-fold Superfamily: TIMP-like Family: The laminin-binding domain of agrin Phyre2 PDB 1z9h chain A domain 1 Region: 249 - 279 Aligned: 31 Modelled: 31 Confidence: 7.6% Identity: 23% Fold: GST C-terminal domain-like Superfamily: GST C-terminal domain-like Family: Glutathione S-transferase (GST), C-terminal domain Phyre2 PDB 1m57 chain H Region: 103 - 182 Aligned: 80 Modelled: 80 Confidence: 7.4% Identity: 6% PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) Phyre2 PDB 3io9 chain B Region: 26 - 40 Aligned: 15 Modelled: 15 Confidence: 7.1% Identity: 33% PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: biml12y in complex with mcl-1 Phyre2 PDB 2b0l chain A domain 1 Region: 430 - 439 Aligned: 10 Modelled: 10 Confidence: 6.6% Identity: 60% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: CodY HTH domain Phyre2 PDB 3dve chain B Region: 167 - 181 Aligned: 15 Modelled: 15 Confidence: 6.6% Identity: 20% PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain complex Phyre2 PDB 1jwh chain C Region: 423 - 439 Aligned: 11 Modelled: 17 Confidence: 5.8% Identity: 73% Fold: Rubredoxin-like Superfamily: Casein kinase II beta subunit Family: Casein kinase II beta subunit Phyre2 PDB 1efy chain A domain 1 Region: 295 - 310 Aligned: 16 Modelled: 16 Confidence: 5.8% Identity: 31% Fold: Domain of poly(ADP-ribose) polymerase Superfamily: Domain of poly(ADP-ribose) polymerase Family: Domain of poly(ADP-ribose) polymerase Phyre2 PDB 2rd6 chain A domain 1 Region: 295 - 310 Aligned: 16 Modelled: 16 Confidence: 5.7% Identity: 31% Fold: Domain of poly(ADP-ribose) polymerase Superfamily: Domain of poly(ADP-ribose) polymerase Family: Domain of poly(ADP-ribose) polymerase Phyre2 PDB 1cw5 chain A Region: 401 - 409 Aligned: 9 Modelled: 9 Confidence: 5.6% Identity: 67% PDB header:toxin Chain: A: PDB Molecule:type iia bacteriocin carnobacteriocin b2; PDBTitle: solution structure of carnobacteriocin b2 Phyre2 PDB 2bbj chain B Region: 333 - 364 Aligned: 32 Modelled: 32 Confidence: 5.5% Identity: 16% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 1 c2pidB_ 2 c2wwaC_ 3 c3ipdB_ 4 c2vqzB_ 5 c2l9uA_ 6 d2axtj1 7 c3d9wA_ 8 d1qf8a_ 9 c3dvjB_ 10 d1jb3a_ 11 d1z9ha1 12 c1m57H_ 13 c3io9B_ 14 d2b0la1 15 c3dveB_ 16 d1jwhc_ 17 d1efya1 18 d2rd6a1 19 c1cw5A_ 20 c2bbjB_ 21 22 23 24 25 26 27

Detailed template information

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

1 c2pidB_ 15.3 17 PDB header:ligase Chain: B: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: crystal structure of human mitochondrial tyrosyl-trna synthetase in2 complex with an adenylate analog 2 c2wwaC_ 13.4 38 PDB header:ribosome Chain: C: PDB Molecule:protein transport protein seb2; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome 3 c3ipdB_ 12.2 15 PDB header:exocytosis Chain: B: PDB Molecule:syntaxin-1a; PDBTitle: helical extension of the neuronal snare complex into the2 membrane, spacegroup i 21 21 21 4 c2vqzB_ 11.8 22 PDB header:transcription Chain: B: PDB Molecule:polymerase basic protein 2; PDBTitle: structure of the cap-binding domain of influenza virus2 polymerase subunit pb2 with bound m7gtp 5 c2l9uA_ 10.9 44 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 6 d2axtj1 10.6 47 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like 7 c3d9wA_ 10.2 30 PDB header:transferase Chain: A: PDB Molecule:putative acetyltransferase; PDBTitle: crystal structure analysis of nocardia farcinica arylamine2 n-acetyltransferase 8 d1qf8a_ 8.8 73 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 9 c3dvjB_ 8.7 20 PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain (without cloning2 artifact, hm to tv) complex 10 d1jb3a_ 8.5 44 Fold:OB-fold Superfamily:TIMP-like Family:The laminin-binding domain of agrin 11 d1z9ha1 7.6 23 Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain 12 c1m57H_ 7.4 6 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 13 c3io9B_ 7.1 33 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-like protein 11; PDBTitle: biml12y in complex with mcl-1 14 d2b0la1 6.6 60 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CodY HTH domain 15 c3dveB_ 6.6 20 PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain complex 16 d1jwhc_ 5.8 73 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 17 d1efya1 5.8 31 Fold:Domain of poly(ADP-ribose) polymerase Superfamily:Domain of poly(ADP-ribose) polymerase Family:Domain of poly(ADP-ribose) polymerase 18 d2rd6a1 5.7 31 Fold:Domain of poly(ADP-ribose) polymerase Superfamily:Domain of poly(ADP-ribose) polymerase Family:Domain of poly(ADP-ribose) polymerase 19 c1cw5A_ 5.6 67 PDB header:toxin Chain: A: PDB Molecule:type iia bacteriocin carnobacteriocin b2; PDBTitle: solution structure of carnobacteriocin b2 20 c2bbjB_ 5.5 16 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 21 c3rmrA_ not modelled 5.5 37 PDB header:protein binding Chain: A: PDB Molecule:avirulence protein; PDBTitle: crystal structure of hyaloperonospora arabidopsidis atr1 effector2 domain 22 d1eysh2 not modelled 5.5 26 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 23 c2hqlB_ not modelled 5.4 22 PDB header:dna binding protein Chain: B: PDB Molecule:hypothetical protein mg376 homolog; PDBTitle: crystal structure of a small single-stranded dna binding2 protein from mycoplasma pneumoniae 24 d1y14b2 not modelled 5.3 33 Fold:Dodecin subunit-like Superfamily:N-terminal, heterodimerisation domain of RBP7 (RpoE) Family:N-terminal, heterodimerisation domain of RBP7 (RpoE) 25 c2kegA_ not modelled 5.3 35 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnk; PDBTitle: nmr structure of plantaricin k in dpc-micelles 26 c2x11B_ not modelled 5.2 36 PDB header:receptor/signaling protein Chain: B: PDB Molecule:ephrin-a5; PDBTitle: crystal structure of the complete epha2 ectodomain in2 complex with ephrin a5 receptor binding domain 27 d1shxa1 not modelled 5.2 36 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Ephrin ectodomain

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