Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	D	N	A	Q	L	T	G	L	C	D	R	F	R	G	F	Y	P	V	V	I	D	V	E	T	A	G	F	N	A	K	T	D	A	L	L	E	I	A	A	I	T	L	K	M	D	E	Q	G	W	L	M	P	D	T	T	L	H	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		H	V	E	P	F	V	G	A	N	L	Q	P	E	A	L	A	F	N	G	I	D	P	N	D	P	D	R	G	A	V	S	E	Y	E	A	L	H	E	I	F	K	V	V	R	K	G	I	K	A	S	G	C	N	R	A	I	M	V	A	H
Secondary structure
SS confidence
Disorder								?			?																	?	?																					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	A	N	F	D	H	S	F	M	M	A	A	A	E	R	A	S	L	K	R	N	P	F	H	P	F	A	T	F	D	T	A	A	L	A	G	L	A	L	G	Q	T	V	L	S	K	A	C	Q	T	A	G	M	D	F	D	S	T	Q	A
Secondary structure
SS confidence
Disorder																																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.
Sequence		H	S	A	L	Y	D	T	E	R	T	A	V	L	F	C	E	I	V	N	R	W	K	R	L	G	G	W	P	L	S	A	A	E	E	V
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 2f96 chain A domain 1 Region: 9 - 208 Aligned: 200 Modelled: 197 Confidence: 100.0% Identity: 62% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2is3 chain B Region: 7 - 211 Aligned: 172 Modelled: 205 Confidence: 100.0% Identity: 90% PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t Phyre2 PDB 2qxf chain A domain 1 Region: 16 - 204 Aligned: 172 Modelled: 189 Confidence: 100.0% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1zbu chain B Region: 17 - 200 Aligned: 174 Modelled: 175 Confidence: 100.0% Identity: 20% PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease Phyre2 PDB 1zbh chain A Region: 19 - 199 Aligned: 171 Modelled: 176 Confidence: 100.0% Identity: 21% 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 3cm6 chain A Region: 19 - 199 Aligned: 174 Modelled: 176 Confidence: 100.0% Identity: 15% 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 1y97 chain A domain 1 Region: 15 - 204 Aligned: 181 Modelled: 182 Confidence: 100.0% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2xri chain A Region: 19 - 200 Aligned: 177 Modelled: 181 Confidence: 100.0% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3 Phyre2 PDB 2p1j chain B Region: 19 - 207 Aligned: 169 Modelled: 189 Confidence: 100.0% Identity: 27% 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 2gui chain A domain 1 Region: 19 - 197 Aligned: 163 Modelled: 179 Confidence: 100.0% Identity: 23% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1w0h chain A Region: 19 - 200 Aligned: 176 Modelled: 178 Confidence: 100.0% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3b6o chain A domain 1 Region: 19 - 204 Aligned: 178 Modelled: 186 Confidence: 100.0% Identity: 11% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3u6f chain A Region: 19 - 204 Aligned: 179 Modelled: 186 Confidence: 100.0% Identity: 12% PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant Phyre2 PDB 1j9a chain A Region: 12 - 204 Aligned: 176 Modelled: 189 Confidence: 100.0% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 3tr8 chain A Region: 14 - 204 Aligned: 174 Modelled: 191 Confidence: 100.0% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii Phyre2 PDB 2igi chain A domain 1 Region: 19 - 204 Aligned: 169 Modelled: 186 Confidence: 100.0% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 2gbz chain A Region: 19 - 206 Aligned: 171 Modelled: 188 Confidence: 99.9% Identity: 19% 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 1wlj chain A Region: 19 - 210 Aligned: 163 Modelled: 190 Confidence: 99.9% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: DnaQ-like 3'-5' exonuclease Phyre2 PDB 1uoc chain A Region: 4 - 203 Aligned: 194 Modelled: 195 Confidence: 99.8% Identity: 12% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: CAF1-like ribonuclease Phyre2 PDB 2d5r chain A domain 1 Region: 4 - 206 Aligned: 196 Modelled: 198 Confidence: 99.7% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: CAF1-like ribonuclease Phyre2 1 d2f96a1 2 c2is3B_ 3 d2qxfa1 4 c1zbuB_ 5 c1zbhA_ 6 c3cm6A_ 7 d1y97a1 8 c2xriA_ 9 c2p1jB_ 10 d2guia1 11 d1w0ha_ 12 d3b6oa1 13 c3u6fA_ 14 d1j9aa_ 15 c3tr8A_ 16 d2igia1 17 c2gbzA_ 18 d1wlja_ 19 d1uoca_ 20 d2d5ra1 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

Detailed template information

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

1 d2f96a1 100.0 62 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 2 c2is3B_ 100.0 90 PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease t; PDBTitle: crystal structure of escherichia coli rnase t 3 d2qxfa1 100.0 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 4 c1zbuB_ 100.0 20 PDB header:hydrolase Chain: B: PDB Molecule:3'-5' exonuclease eri1; PDBTitle: crystal structure of full-length 3'-exonuclease 5 c1zbhA_ 100.0 21 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 6 c3cm6A_ 100.0 15 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 7 d1y97a1 100.0 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 8 c2xriA_ 100.0 16 PDB header:hydrolase Chain: A: PDB Molecule:eri1 exoribonuclease 3; PDBTitle: crystal structure of human eri1 exoribonuclease 3 9 c2p1jB_ 100.0 27 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 10 d2guia1 100.0 23 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 11 d1w0ha_ 100.0 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 12 d3b6oa1 100.0 11 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 13 c3u6fA_ 100.0 12 PDB header:hydrolase/dna Chain: A: PDB Molecule:three prime repair exonuclease 1; PDBTitle: mouse trex1 d200n mutant 14 d1j9aa_ 100.0 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 15 c3tr8A_ 100.0 18 PDB header:hydrolase Chain: A: PDB Molecule:oligoribonuclease; PDBTitle: structure of an oligoribonuclease (orn) from coxiella burnetii 16 d2igia1 100.0 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 17 c2gbzA_ 99.9 19 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 d1wlja_ 99.9 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 19 d1uoca_ 99.8 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 20 d2d5ra1 99.7 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 21 c2p51A_ not modelled 99.7 15 PDB header:hydrolase, gene regulation Chain: A: PDB Molecule:spcc18.06c protein; PDBTitle: crystal structure of the s. pombe pop2p deadenylation2 subunit 22 c3d45B_ not modelled 99.4 19 PDB header:hydrolase Chain: B: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of mouse parn in complex with m7gpppg 23 c2a1sC_ not modelled 99.4 24 PDB header:hydrolase Chain: C: PDB Molecule:poly(a)-specific ribonuclease parn; PDBTitle: crystal structure of native parn nuclease domain 24 d1kfsa1 not modelled 99.3 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 25 d1x9ma1 not modelled 99.1 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 26 c2kzzA_ not modelled 99.1 16 PDB header:transferase/dna Chain: A: PDB Molecule:protein (dna polymerase i); PDBTitle: klenow fragment with normal substrate and zinc only 27 c1njzA_ not modelled 98.9 17 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase i; PDBTitle: cytosine-thymine mismatch at the polymerase active site 28 d2hhva1 not modelled 98.8 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 29 c1tk0A_ not modelled 98.7 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 30 c1yt3A_ not modelled 98.4 19 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 31 d1wn7a1 not modelled 98.4 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 32 d1qhta1 not modelled 98.4 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 33 d1tgoa1 not modelled 98.3 21 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 34 d1yt3a3 not modelled 98.3 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 35 d1d5aa1 not modelled 98.2 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 36 c3iayA_ not modelled 98.0 19 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase delta catalytic subunit; PDBTitle: ternary complex of dna polymerase delta 37 c2gv9B_ not modelled 98.0 18 PDB header:transferase Chain: B: PDB Molecule:dna polymerase; PDBTitle: crystal structure of the herpes simplex virus type 1 dna polymerase 38 c2e6mA_ not modelled 97.9 12 PDB header:hydrolase Chain: A: PDB Molecule:werner syndrome atp-dependent helicase homolog; PDBTitle: structure of mouse werner exonuclease domain 39 c4ktqA_ not modelled 97.8 19 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 40 c3cymA_ not modelled 97.8 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bad_0989; PDBTitle: crystal structure of protein bad_0989 from bifidobacterium2 adolescentis 41 d1s5ja1 not modelled 97.5 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 42 c1d5aA_ not modelled 97.3 21 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 d1ih7a1 not modelled 97.2 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 44 c2hbkA_ not modelled 97.2 15 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 45 c3sahA_ not modelled 97.1 16 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 46 d2hbka2 not modelled 97.1 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 47 d1q8ia1 not modelled 96.9 18 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 48 c2vwkA_ not modelled 96.8 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 49 d1noya_ not modelled 96.4 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 50 c1s5jA_ not modelled 92.8 19 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 51 c1q8iA_ not modelled 91.7 18 PDB header:transferase Chain: A: PDB Molecule:dna polymerase ii; PDBTitle: crystal structure of escherichia coli dna polymerase ii 52 d1vk0a_ not modelled 83.6 11 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 53 c2dtuA_ not modelled 81.9 13 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 54 c3ikmD_ not modelled 81.5 17 PDB header:transferase Chain: D: PDB Molecule:dna polymerase subunit gamma-1; PDBTitle: crystal structure of human mitochondrial dna polymerase2 holoenzyme 55 c1cmwA_ not modelled 66.1 22 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 56 c3mx2A_ not modelled 56.8 16 PDB header:nuclear protein Chain: A: PDB Molecule:nucleoprotein; PDBTitle: lassa fever virus nucleoprotein complexed with dttp 57 d2py5a1 not modelled 32.0 33 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 58 d1fnoa4 not modelled 7.7 15 Fold:Phosphorylase/hydrolase-like Superfamily:Zn-dependent exopeptidases Family:Bacterial dinuclear zinc exopeptidases 59 c2ex3I_ not modelled 6.5 19 PDB header:transferase/replication Chain: I: PDB Molecule:dna polymerase; PDBTitle: bacteriophage phi29 dna polymerase bound to terminal protein

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