Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	L	R	L	S	A	L	A	L	G	T	T	L	L	V	G	C	A	S	S	G	T	D	Q	Q	G	R	S	D	P	L	E	G	F	N	R	T	M	Y	N	F	N	F	N	V	L	D	P	Y	I	V	R	P	V	A	V	A	W	R
Secondary structure
SS confidence
Disorder		?	?	?																?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	Y	V	P	Q	P	A	R	N	G	L	S	N	F	T	G	N	L	E	E	P	A	V	M	V	N	Y	F	L	Q	G	D	P	Y	Q	G	M	V	H	F	T	R	F	F	L	N	T	I	L	G	M	G	G	F	I	D	V	A	G	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	N	P	K	L	Q	R	T	E	P	H	R	F	G	S	T	L	G	H	Y	G	V	G	Y	G	P	Y	V	Q	L	P	F	Y	G	S	F	T	L	R	D	D	G	G	D	M	A	D	G	F	Y	P	V	L	S	W	L	T	W	P	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	V	G	K	W	T	L	E	G	I	E	T	R	A	Q	L	L	D	S	D	G	L	L	R	Q	S	S	D	P	Y	I	M	V	R	E	A	Y	F	Q	R	H	D	F	I	A	N	G	G	E	L	K	P	Q	E	N	P	N	A	Q	A
Secondary structure
SS confidence
Disorder																		?	?																											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.
Sequence		I	Q	D	D	L	K	D	I	D	S	E
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 3kuz chain A Region: 136 - 150 Aligned: 15 Modelled: 15 Confidence: 38.4% Identity: 33% PDB header:signaling protein Chain: A: PDB Molecule:plexin-c1; PDBTitle: crystal structure of the ubiquitin like domain of plxnc1 Phyre2 PDB 2jph chain A Region: 136 - 150 Aligned: 15 Modelled: 15 Confidence: 38.0% Identity: 53% PDB header:signaling protein, protein binding Chain: A: PDB Molecule:plexin-b1; PDBTitle: nmr solution structure of the rho gtpase binding domain of2 human plexin-b1 Phyre2 PDB 1wjn chain A Region: 135 - 157 Aligned: 23 Modelled: 23 Confidence: 34.3% Identity: 22% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 3h6n chain A Region: 136 - 150 Aligned: 15 Modelled: 14 Confidence: 34.2% Identity: 33% PDB header:signaling protein Chain: A: PDB Molecule:plexin-d1; PDBTitle: crystal structure of the ubiquitin-like domain of plexin d1 Phyre2 PDB 3q3j chain A Region: 136 - 150 Aligned: 15 Modelled: 15 Confidence: 33.3% Identity: 47% PDB header:membrane protein/protein binding Chain: A: PDB Molecule:plexin-a2; PDBTitle: crystal structure of plexin a2 rbd in complex with rnd1 Phyre2 PDB 1z2m chain A domain 1 Region: 134 - 150 Aligned: 17 Modelled: 17 Confidence: 21.7% Identity: 35% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 2odg chain C domain 1 Region: 129 - 146 Aligned: 18 Modelled: 18 Confidence: 17.2% Identity: 22% Fold: LEM/SAP HeH motif Superfamily: LEM domain Family: LEM domain Phyre2 PDB 1we7 chain A Region: 134 - 157 Aligned: 24 Modelled: 24 Confidence: 16.2% Identity: 21% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 2wx3 chain A Region: 187 - 220 Aligned: 34 Modelled: 34 Confidence: 14.2% Identity: 29% PDB header:structural protein Chain: A: PDB Molecule:mrna-decapping enzyme 1a; PDBTitle: asymmetric trimer of the human dcp1a c-terminal domain Phyre2 PDB 1we6 chain A Region: 134 - 157 Aligned: 24 Modelled: 24 Confidence: 14.1% Identity: 33% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 1wzi chain A Region: 138 - 154 Aligned: 17 Modelled: 17 Confidence: 13.6% Identity: 29% PDB header:oxidoreductase Chain: A: PDB Molecule:malate dehydrogenase; PDBTitle: structural basis for alteration of cofactor specificity of2 malate dehydrogenase from thermus flavus Phyre2 PDB 3su8 chain X Region: 136 - 150 Aligned: 15 Modelled: 15 Confidence: 13.3% Identity: 53% PDB header:apoptosis/signaling protein Chain: X: PDB Molecule:plexin-b1; PDBTitle: crystal structure of a truncated intracellular domain of plexin-b1 in2 complex with rac1 Phyre2 PDB 157l chain A Region: 49 - 102 Aligned: 54 Modelled: 54 Confidence: 12.9% Identity: 17% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: Phage lysozyme Phyre2 PDB 2aga chain A Region: 82 - 98 Aligned: 17 Modelled: 17 Confidence: 12.8% Identity: 24% PDB header:transcription Chain: A: PDB Molecule:machado-joseph disease protein 1; PDBTitle: de-ubiquitinating function of ataxin-3: insights from the2 solution structure of the josephin domain Phyre2 PDB 1ogw chain A Region: 134 - 154 Aligned: 21 Modelled: 21 Confidence: 12.1% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 3ig3 chain A Region: 136 - 151 Aligned: 16 Modelled: 16 Confidence: 10.1% Identity: 44% PDB header:signaling protein, membrane protein Chain: A: PDB Molecule:plxna3 protein; PDBTitle: crystal strucure of mouse plexin a3 intracellular domain Phyre2 PDB 1zkh chain A domain 1 Region: 134 - 150 Aligned: 17 Modelled: 17 Confidence: 9.7% Identity: 24% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ubiquitin-related Phyre2 PDB 1p37 chain A Region: 49 - 102 Aligned: 54 Modelled: 54 Confidence: 9.7% Identity: 20% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: Phage lysozyme Phyre2 PDB 1y7t chain A domain 2 Region: 138 - 153 Aligned: 16 Modelled: 16 Confidence: 9.4% Identity: 31% Fold: LDH C-terminal domain-like Superfamily: LDH C-terminal domain-like Family: Lactate & malate dehydrogenases, C-terminal domain Phyre2 PDB 1i0z chain A domain 2 Region: 138 - 153 Aligned: 16 Modelled: 16 Confidence: 9.4% Identity: 31% Fold: LDH C-terminal domain-like Superfamily: LDH C-terminal domain-like Family: Lactate & malate dehydrogenases, C-terminal domain Phyre2 1 c3kuzA_ 2 c2jphA_ 3 d1wjna_ 4 c3h6nA_ 5 c3q3jA_ 6 d1z2ma1 7 d2odgc1 8 d1we7a_ 9 c2wx3A_ 10 d1we6a_ 11 c1wziA_ 12 c3su8X_ 13 d157la_ 14 c2agaA_ 15 d1ogwa_ 16 c3ig3A_ 17 d1zkha1 18 d1p37a_ 19 d1y7ta2 20 d1i0za2 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

Detailed template information

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

1 c3kuzA_ 38.4 33 PDB header:signaling protein Chain: A: PDB Molecule:plexin-c1; PDBTitle: crystal structure of the ubiquitin like domain of plxnc1 2 c2jphA_ 38.0 53 PDB header:signaling protein, protein binding Chain: A: PDB Molecule:plexin-b1; PDBTitle: nmr solution structure of the rho gtpase binding domain of2 human plexin-b1 3 d1wjna_ 34.3 22 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 4 c3h6nA_ 34.2 33 PDB header:signaling protein Chain: A: PDB Molecule:plexin-d1; PDBTitle: crystal structure of the ubiquitin-like domain of plexin d1 5 c3q3jA_ 33.3 47 PDB header:membrane protein/protein binding Chain: A: PDB Molecule:plexin-a2; PDBTitle: crystal structure of plexin a2 rbd in complex with rnd1 6 d1z2ma1 21.7 35 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 7 d2odgc1 17.2 22 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 8 d1we7a_ 16.2 21 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 9 c2wx3A_ 14.2 29 PDB header:structural protein Chain: A: PDB Molecule:mrna-decapping enzyme 1a; PDBTitle: asymmetric trimer of the human dcp1a c-terminal domain 10 d1we6a_ 14.1 33 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 11 c1wziA_ 13.6 29 PDB header:oxidoreductase Chain: A: PDB Molecule:malate dehydrogenase; PDBTitle: structural basis for alteration of cofactor specificity of2 malate dehydrogenase from thermus flavus 12 c3su8X_ 13.3 53 PDB header:apoptosis/signaling protein Chain: X: PDB Molecule:plexin-b1; PDBTitle: crystal structure of a truncated intracellular domain of plexin-b1 in2 complex with rac1 13 d157la_ 12.9 17 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme 14 c2agaA_ 12.8 24 PDB header:transcription Chain: A: PDB Molecule:machado-joseph disease protein 1; PDBTitle: de-ubiquitinating function of ataxin-3: insights from the2 solution structure of the josephin domain 15 d1ogwa_ 12.1 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 16 c3ig3A_ 10.1 44 PDB header:signaling protein, membrane protein Chain: A: PDB Molecule:plxna3 protein; PDBTitle: crystal strucure of mouse plexin a3 intracellular domain 17 d1zkha1 9.7 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 18 d1p37a_ 9.7 20 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme 19 d1y7ta2 9.4 31 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 20 d1i0za2 9.4 31 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 21 c3m62B_ not modelled 9.2 25 PDB header:ligase/protein binding Chain: B: PDB Molecule:uv excision repair protein rad23; PDBTitle: crystal structure of ufd2 in complex with the ubiquitin-like (ubl)2 domain of rad23 22 d2f2qa1 not modelled 9.1 19 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme 23 c3hm6X_ not modelled 9.0 50 PDB header:signaling protein Chain: X: PDB Molecule:plexin-b1; PDBTitle: crystal structure of the cytoplasmic domain of human plexin b1 24 d1v5oa_ not modelled 8.3 44 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 25 d1j8ca_ not modelled 8.3 35 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 26 d1b8pa2 not modelled 8.0 31 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 27 c3jrnA_ not modelled 7.6 27 PDB header:plant protein Chain: A: PDB Molecule:at1g72930 protein; PDBTitle: crystal structure of tir domain from arabidopsis thaliana 28 d1oqya4 not modelled 7.3 13 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 29 d9ldta2 not modelled 7.0 25 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 30 d2c5lc1 not modelled 6.8 13 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD 31 c2o4wA_ not modelled 6.7 20 PDB header:hydrolase Chain: A: PDB Molecule:lysozyme; PDBTitle: t4 lysozyme circular permutant 32 d1wxva1 not modelled 6.7 31 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 33 d1v5ta_ not modelled 6.7 12 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 34 d1icha_ not modelled 6.4 29 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 35 c1ichA_ not modelled 6.4 29 PDB header:apoptosis Chain: A: PDB Molecule:tumor necrosis factor receptor-1; PDBTitle: solution structure of the tumor necrosis factor receptor-12 death domain 36 c3pbpL_ not modelled 6.1 25 PDB header:transport protein,structural protein Chain: L: PDB Molecule:nucleoporin nup159; PDBTitle: structure of the yeast heterotrimeric nup82-nup159-nup116 nucleoporin2 complex 37 d1z2ma2 not modelled 6.1 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 38 d1sifa_ not modelled 6.1 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 39 d2ihoa2 not modelled 6.0 50 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:MOA C-terminal domain-like 40 d1uela_ not modelled 6.0 16 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 41 c2kj6A_ not modelled 5.9 19 PDB header:chaperone Chain: A: PDB Molecule:tubulin folding cofactor b; PDBTitle: nmr solution structure of a tubulin folding cofactor b2 obtained from arabidopsis thaliana: northeast structural3 genomics consortium target ar3436a 42 c2k25A_ not modelled 5.9 29 PDB header:unknown function Chain: A: PDB Molecule:ubb; PDBTitle: automated nmr structure of the ubb by fapsy 43 d1l64a_ not modelled 5.7 16 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme 44 c2l7rA_ not modelled 5.7 29 PDB header:protein binding Chain: A: PDB Molecule:ubiquitin-like protein fubi; PDBTitle: solution nmr structure of n-terminal ubiquitin-like domain of fubi, a2 ribosomal protein s30 precursor from homo sapiens. northeast3 structural genomics consortium (nesg) target hr6166 45 d1ldma2 not modelled 5.7 25 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 46 d2bh1a1 not modelled 5.6 25 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Cyto-EpsL domain 47 c2kanA_ not modelled 5.6 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ar3433a; PDBTitle: solution nmr structure of ubiquitin-like domain of2 arabidopsis thaliana protein at2g32350. northeast3 structural genomics consortium target ar3433a 48 d1wx8a1 not modelled 5.6 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 49 d2ldxa2 not modelled 5.4 19 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 50 d1jtma_ not modelled 5.4 18 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme 51 c1yx5B_ not modelled 5.3 29 PDB header:hydrolase Chain: B: PDB Molecule:ubiquitin; PDBTitle: solution structure of s5a uim-1/ubiquitin complex 52 d1qbaa2 not modelled 5.3 12 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Bacterial chitobiase, n-terminal domain 53 d2g7ja1 not modelled 5.1 30 Fold:Secretion chaperone-like Superfamily:YgaC/TfoX-N like Family:YgaC-like 54 d1bt0a_ not modelled 5.1 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related

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