Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	R	I	I	D	T	E	T	C	G	L	Q	G	G	I	V	E	I	A	S	V	D	V	I	D	G	K	I	V	N	P	M	S	H	L	V	R	P	D	R	P	I	S	P	Q	A	M	A	I	H	R	I	T	E	A	M	V	A	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	P	W	I	E	D	V	I	P	H	Y	Y	G	S	E	W	Y	V	A	H	N	A	S	F	D	R	R	V	L	P	E	M	P	G	E	W	I	C	T	M	K	L	A	R	R	L	W	P	G	I	K	Y	S	N	M	A	L	Y	K	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	K	L	N	V	Q	T	P	P	G	L	H	H	H	R	A	L	Y	D	C	Y	I	T	A	A	L	L	I	D	I	M	N	T	S	G	W	T	A	E	Q	M	A	D	I	T	G	R	P	S	L	M	T	T	F	T	F	G	K	Y	R
Secondary structure
SS confidence
Disorder								?																										?															?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220
Sequence		G	K	A	V	S	D	V	A	E	R	D	P	G	Y	L	R	W	L	F	N	N	L	D	S	M	S	P	E	L	R	L	T	L	K	H	Y	L	E	N	T
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 1y97 chain A domain 1 Region: 2 - 153 Aligned: 145 Modelled: 152 Confidence: 100.0% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2qxf chain A domain 1 Region: 2 - 180 Aligned: 172 Modelled: 172 Confidence: 100.0% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3u6f chain A Region: 2 - 153 Aligned: 149 Modelled: 149 Confidence: 100.0% Identity: 18% PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant Phyre2 PDB 1zbh chain A Region: 2 - 153 Aligned: 149 Modelled: 149 Confidence: 100.0% Identity: 17% PDB header:hydrolase/rna Chain: A: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: 3'-end specific recognition of histone mrna stem-loop by 3'-2 exonuclease Phyre2 PDB 1zbu chain B Region: 2 - 153 Aligned: 149 Modelled: 148 Confidence: 100.0% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease Phyre2 PDB 2gui chain A domain 1 Region: 2 - 150 Aligned: 146 Modelled: 149 Confidence: 100.0% Identity: 30% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2p1j chain B Region: 2 - 156 Aligned: 150 Modelled: 155 Confidence: 100.0% Identity: 34% PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii polc-type; PDBTitle: crystal structure of a polc-type dna polymerase iii2 exonuclease domain from thermotoga maritima Phyre2 PDB 3cm6 chain A Region: 2 - 156 Aligned: 155 Modelled: 155 Confidence: 100.0% Identity: 17% PDB header:hydrolase, apoptosis Chain: A: PDB Molecule:cell death-related nuclease 4; PDBTitle: crystal structure of cell-death related nuclease 4 (crn-4)2 bound with er Phyre2 PDB 3b6o chain A domain 1 Region: 2 - 153 Aligned: 148 Modelled: 152 Confidence: 100.0% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1wlj chain A Region: 2 - 152 Aligned: 148 Modelled: 151 Confidence: 100.0% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1j9a chain A Region: 2 - 156 Aligned: 144 Modelled: 153 Confidence: 100.0% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3tr8 chain A Region: 2 - 153 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii Phyre2 PDB 1w0h chain A Region: 2 - 156 Aligned: 152 Modelled: 155 Confidence: 100.0% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2xri chain A Region: 2 - 153 Aligned: 149 Modelled: 152 Confidence: 100.0% Identity: 17% PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3 Phyre2 PDB 2f96 chain A domain 1 Region: 1 - 153 Aligned: 151 Modelled: 152 Confidence: 100.0% Identity: 22% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2igi chain A domain 1 Region: 2 - 156 Aligned: 144 Modelled: 155 Confidence: 100.0% Identity: 19% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2gbz chain A Region: 2 - 152 Aligned: 140 Modelled: 140 Confidence: 99.9% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: the crystal structure of xc847 from xanthomonas campestris: a 3-52 oligoribonuclease of dnaq fold family with a novel opposingly-shifted3 helix Phyre2 PDB 2is3 chain B Region: 3 - 153 Aligned: 131 Modelled: 138 Confidence: 99.9% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t Phyre2 PDB 1uoc chain A Region: 2 - 152 Aligned: 148 Modelled: 151 Confidence: 99.4% Identity: 9% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: CAF1-like ribonuclease Phyre2 PDB 1kfs chain A domain 1 Region: 2 - 156 Aligned: 141 Modelled: 141 Confidence: 99.1% Identity: 19% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 1 d1y97a1 2 d2qxfa1 3 c3u6fA_ 4 c1zbhA_ 5 c1zbuB_ 6 d2guia1 7 c2p1jB_ 8 c3cm6A_ 9 d3b6oa1 10 d1wlja_ 11 d1j9aa_ 12 c3tr8A_ 13 d1w0ha_ 14 c2xriA_ 15 d2f96a1 16 d2igia1 17 c2gbzA_ 18 c2is3B_ 19 d1uoca_ 20 d1kfsa1 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

Detailed template information

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

1 d1y97a1 100.0 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 2 d2qxfa1 100.0 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 3 c3u6fA_ 100.0 18 PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant 4 c1zbhA_ 100.0 17 PDB header:hydrolase/rna Chain: A: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: 3'-end specific recognition of histone mrna stem-loop by 3'-2 exonuclease 5 c1zbuB_ 100.0 18 PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease 6 d2guia1 100.0 30 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 7 c2p1jB_ 100.0 34 PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii polc-type; PDBTitle: crystal structure of a polc-type dna polymerase iii2 exonuclease domain from thermotoga maritima 8 c3cm6A_ 100.0 17 PDB header:hydrolase, apoptosis Chain: A: PDB Molecule:cell death-related nuclease 4; PDBTitle: crystal structure of cell-death related nuclease 4 (crn-4)2 bound with er 9 d3b6oa1 100.0 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 10 d1wlja_ 100.0 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 11 d1j9aa_ 100.0 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 12 c3tr8A_ 100.0 17 PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii 13 d1w0ha_ 100.0 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 14 c2xriA_ 100.0 17 PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3 15 d2f96a1 100.0 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 16 d2igia1 100.0 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 17 c2gbzA_ 99.9 16 PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: the crystal structure of xc847 from xanthomonas campestris: a 3-52 oligoribonuclease of dnaq fold family with a novel opposingly-shifted3 helix 18 c2is3B_ 99.9 21 PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t 19 d1uoca_ 99.4 9 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 20 d1kfsa1 99.1 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 21 d2d5ra1 not modelled 99.1 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 22 d1x9ma1 not modelled 99.1 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 23 c2p51A_ not modelled 99.0 15 PDB header:hydrolase, gene regulation Chain: A: PDB Molecule:spcc18.06c protein; PDBTitle: crystal structure of the s. pombe pop2p deadenylation2 subunit 24 c2kzzA_ not modelled 99.0 18 PDB header:transferase/dna Chain: A: PDB Molecule:protein (dna polymerase i); PDBTitle: klenow fragment with normal substrate and zinc only 25 c1tk0A_ not modelled 98.8 20 PDB header:transferase/electron transport/dna Chain: A: PDB Molecule:dna polymerase; PDBTitle: t7 dna polymerase ternary complex with 8 oxo guanosine and2 ddctp at the insertion site 26 c1njzA_ not modelled 98.8 14 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase i; PDBTitle: cytosine-thymine mismatch at the polymerase active site 27 c3d45B_ not modelled 98.6 23 PDB header:hydrolase Chain: B: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of mouse parn in complex with m7gpppg 28 d2hhva1 not modelled 98.5 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 29 c2a1sC_ not modelled 98.5 23 PDB header:hydrolase Chain: C: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of native parn nuclease domain 30 d1d5aa1 not modelled 98.0 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 31 d1wn7a1 not modelled 97.9 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 32 c2gv9B_ not modelled 97.9 12 PDB header:transferase Chain: B: PDB Molecule:dna polymerase; PDBTitle: crystal structure of the herpes simplex virus type 1 dna polymerase 33 d1qhta1 not modelled 97.9 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 34 c1yt3A_ not modelled 97.7 22 PDB header:hydrolase,translation Chain: A: PDB Molecule:ribonuclease d; PDBTitle: crystal structure of escherichia coli rnase d, an2 exoribonuclease involved in structured rna processing 35 d1tgoa1 not modelled 97.7 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 36 d1noya_ not modelled 97.6 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 37 d1q8ia1 not modelled 97.5 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 38 c3iayA_ not modelled 97.5 21 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase delta catalytic subunit; PDBTitle: ternary complex of dna polymerase delta 39 d1ih7a1 not modelled 97.3 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 40 c2e6mA_ not modelled 97.3 12 PDB header:hydrolase Chain: A: PDB Molecule:werner syndrome atp-dependent helicase homolog; PDBTitle: structure of mouse werner exonuclease domain 41 c2dtuA_ not modelled 97.2 18 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase; PDBTitle: crystal structure of the beta hairpin loop deletion variant2 of rb69 gp43 in complex with dna containing an abasic site3 analog 42 c1d5aA_ not modelled 97.1 16 PDB header:transferase Chain: A: PDB Molecule:protein (dna polymerase); PDBTitle: crystal structure of an archaebacterial dna polymerase2 d.tok. deposition of second native structure at 2.43 angstrom 43 c3cymA_ not modelled 97.1 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bad_0989; PDBTitle: crystal structure of protein bad_0989 from bifidobacterium2 adolescentis 44 c2vwkA_ not modelled 97.0 18 PDB header:dna replication Chain: A: PDB Molecule:dna polymerase; PDBTitle: uracil recognition in archaeal dna polymerases captured by2 x-ray crystallography. v93q polymerase variant 45 d1yt3a3 not modelled 96.9 21 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 46 c1q8iA_ not modelled 96.6 20 PDB header:transferase Chain: A: PDB Molecule:dna polymerase ii; PDBTitle: crystal structure of escherichia coli dna polymerase ii 47 d1s5ja1 not modelled 96.4 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 48 c4ktqA_ not modelled 96.4 16 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 49 d2hbka2 not modelled 94.6 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 50 d1vk0a_ not modelled 93.0 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 51 c1s5jA_ not modelled 92.1 16 PDB header:transferase Chain: A: PDB Molecule:dna polymerase i; PDBTitle: insight in dna replication: the crystal structure of dna2 polymerase b1 from the archaeon sulfolobus solfataricus 52 c3ikmD_ not modelled 91.9 18 PDB header:transferase Chain: D: PDB Molecule:dna polymerase subunit gamma-1; PDBTitle: crystal structure of human mitochondrial dna polymerase2 holoenzyme 53 c2hbkA_ not modelled 85.4 20 PDB header:hydrolase, gene regulation Chain: A: PDB Molecule:exosome complex exonuclease rrp6; PDBTitle: structure of the yeast nuclear exosome component, rrp6p,2 reveals an interplay between the active site and the hrdc3 domain; protein in complex with mn 54 c3mx2A_ not modelled 68.9 20 PDB header:nuclear protein Chain: A: PDB Molecule:nucleoprotein; PDBTitle: lassa fever virus nucleoprotein complexed with dttp 55 c3q7cA_ not modelled 68.4 20 PDB header:hydrolase Chain: A: PDB Molecule:nucleoprotein; PDBTitle: exonuclease domain of lassa virus nucleoprotein bound to manganese 56 c1cmwA_ not modelled 64.2 18 PDB header:transferase Chain: A: PDB Molecule:protein (dna polymerase i); PDBTitle: crystal structure of taq dna-polymerase shows a new2 orientation for the structure-specific nuclease domain 57 c3sahA_ not modelled 49.5 21 PDB header:hydrolase Chain: A: PDB Molecule:exosome component 10; PDBTitle: crystal structure of the human rrp6 catalytic domain with y436a2 mutation in the catalytic site 58 d2py5a1 not modelled 17.8 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 59 c1lj2B_ not modelled 9.4 13 PDB header:viral protein/ translation Chain: B: PDB Molecule:nonstructural rna-binding protein 34; PDBTitle: recognition of eif4g by rotavirus nsp3 reveals a basis for2 mrna circularization 60 c3eukC_ not modelled 5.4 14 PDB header:cell cycle Chain: C: PDB Molecule:chromosome partition protein mukb, linker; PDBTitle: crystal structure of muke-mukf(residues 292-443)-mukb(head2 domain)-atpgammas complex, asymmetric dimer 61 c3g6iA_ not modelled 5.3 18 PDB header:unknown function Chain: A: PDB Molecule:putative outer membrane protein, part of carbohydrate PDBTitle: crystal structure of an outer membrane protein, part of a putative2 carbohydrate binding complex (bt_1022) from bacteroides3 thetaiotaomicron vpi-5482 at 1.93 a resolution

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