Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP03018
DateThu Jan 5 10:57:53 GMT 2012
Unique Job ID8d21141b90c64f14

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2is6B_
Top template information
PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex
Confidence and coverage
Confidence:100.0% Coverage: 91%
652 residues ( 91% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MDVSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAV
Secondary structure 
SS confidence 
Disorder  ??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  TFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQL
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  RLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEA
Secondary structure 
SS confidence 
Disorder 
?
??
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  CDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDT
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  GKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENN
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  NGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQS
Secondary structure 
SS confidence 
Disorder  ??????
????
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  RVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNTPTRGIGD
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  RTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQ
Secondary structure 
SS confidence 
Disorder 
????
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  TDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDLMPLQAFLSHAAL
Secondary structure 
SS confidence 
Disorder 
????
???
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  EAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSLDEGGRLEEERRLAY
Secondary structure 
SS confidence 
Disorder  ????????????
?
?
?????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  VGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLRATVSRPVSHQRMG
Secondary structure 
SS confidence 
Disorder 
??????????????
???????????????
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  TPMVENDSGYKLGQRVRHAKFGEGTIVNMEGSGEHSRLQVAFQGQGIKWLVAAYARLESV
Secondary structure 
SS confidence 
Disorder  ?????????
?
????????
Disorder confidence 
 
  
Sequence 
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

RankAligned region

PDB 2is6 chain B

3D model

Region: 2 - 662
Aligned: 652
Modelled: 656
Confidence: 100.0%
Identity: 99%
PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex

Phyre2

PDB 1uaa chain B

3D model

Region: 9 - 640
Aligned: 624
Modelled: 626
Confidence: 100.0%
Identity: 38%
PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (atp-dependent dna helicase rep.);
PDBTitle: e. coli rep helicase/dna complex

Phyre2

PDB 3lfu chain A

3D model

Region: 3 - 647
Aligned: 633
Modelled: 645
Confidence: 100.0%
Identity: 99%
PDB header:hydrolase
Chain: A: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of e. coli uvrd

Phyre2

PDB 1w36 chain E

3D model

Region: 22 - 626
Aligned: 569
Modelled: 580
Confidence: 100.0%
Identity: 25%
PDB header:recombination
Chain: E: PDB Molecule:exodeoxyribonuclease v beta chain;
PDBTitle: recbcd:dna complex

Phyre2

PDB 1pjr chain A

3D model

Region: 4 - 642
Aligned: 613
Modelled: 614
Confidence: 100.0%
Identity: 44%
PDB header:helicase
Chain: A: PDB Molecule:pcra;
PDBTitle: structure of dna helicase

Phyre2

PDB 2pjr chain F

3D model

Region: 4 - 547
Aligned: 540
Modelled: 544
Confidence: 100.0%
Identity: 42%
PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex

Phyre2

PDB 1pjr chain A domain 1

3D model

Region: 1 - 315
Aligned: 313
Modelled: 315
Confidence: 100.0%
Identity: 43%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1w36 chain F

3D model

Region: 33 - 640
Aligned: 596
Modelled: 607
Confidence: 100.0%
Identity: 16%
PDB header:recombination
Chain: F: PDB Molecule:exodeoxyribonuclease v gamma chain;
PDBTitle: recbcd:dna complex

Phyre2

PDB 1uaa chain A domain 2

3D model

Region: 315 - 643
Aligned: 326
Modelled: 329
Confidence: 100.0%
Identity: 38%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1uaa chain A domain 1

3D model

Region: 9 - 313
Aligned: 305
Modelled: 305
Confidence: 100.0%
Identity: 37%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1w36 chain B domain 1

3D model

Region: 13 - 313
Aligned: 299
Modelled: 301
Confidence: 100.0%
Identity: 24%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1pjr chain A domain 2

3D model

Region: 316 - 644
Aligned: 305
Modelled: 329
Confidence: 100.0%
Identity: 46%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1w36 chain B domain 2

3D model

Region: 327 - 646
Aligned: 289
Modelled: 295
Confidence: 100.0%
Identity: 19%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1qhh chain B

3D model

Region: 166 - 424
Aligned: 259
Modelled: 258
Confidence: 100.0%
Identity: 48%
PDB header:hydrolase
Chain: B: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp

Phyre2

PDB 2xzl chain A

3D model

Region: 9 - 614
Aligned: 358
Modelled: 375
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex

Phyre2

PDB 2wjy chain A

3D model

Region: 7 - 614
Aligned: 361
Modelled: 367
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: crystal structure of the complex between human nonsense2 mediated decay factors upf1 and upf2 orthorhombic form

Phyre2

PDB 1qhh chain A

3D model

Region: 1 - 162
Aligned: 162
Modelled: 162
Confidence: 100.0%
Identity: 43%
PDB header:hydrolase
Chain: A: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp

Phyre2

PDB 1w36 chain C domain 2

3D model

Region: 303 - 640
Aligned: 334
Modelled: 338
Confidence: 100.0%
Identity: 17%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 2gk7 chain A

3D model

Region: 7 - 614
Aligned: 358
Modelled: 366
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: structural and functional insights into the human upf1 helicase core

Phyre2

PDB 3e1s chain A

3D model

Region: 9 - 615
Aligned: 312
Modelled: 341
Confidence: 100.0%
Identity: 23%
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2

Phyre2
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c2is6B_
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c1uaaB_
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c3lfuA_
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c1w36E_
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c1pjrA_
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c2pjrF_
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d1pjra1
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c1w36F_
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d1uaaa2
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d1uaaa1
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d1w36b1
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d1pjra2
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d1w36b2
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c1qhhB_
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c2xzlA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2is6B_
100.0 99 PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex
2c1uaaB_
100.0 38 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (atp-dependent dna helicase rep.);
PDBTitle: e. coli rep helicase/dna complex
3c3lfuA_
100.0 99 PDB header:hydrolase
Chain: A: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of e. coli uvrd
4c1w36E_
100.0 25 PDB header:recombination
Chain: E: PDB Molecule:exodeoxyribonuclease v beta chain;
PDBTitle: recbcd:dna complex
5c1pjrA_
100.0 44 PDB header:helicase
Chain: A: PDB Molecule:pcra;
PDBTitle: structure of dna helicase
6c2pjrF_
100.0 42 PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
7d1pjra1
100.0 43 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
8c1w36F_
100.0 16 PDB header:recombination
Chain: F: PDB Molecule:exodeoxyribonuclease v gamma chain;
PDBTitle: recbcd:dna complex
9d1uaaa2
100.0 38 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
10d1uaaa1
100.0 37 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
11d1w36b1
100.0 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
12d1pjra2
100.0 46 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
13d1w36b2
100.0 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
14c1qhhB_
100.0 48 PDB header:hydrolase
Chain: B: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
15c2xzlA_
100.0 22 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex
16c2wjyA_
100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: crystal structure of the complex between human nonsense2 mediated decay factors upf1 and upf2 orthorhombic form
17c1qhhA_
100.0 43 PDB header:hydrolase
Chain: A: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
18d1w36c2
100.0 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
19c2gk7A_
100.0 22 PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: structural and functional insights into the human upf1 helicase core
20c3e1sA_
100.0 23 PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2
21c1w36G_
not modelled 100.0 32 PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex
22c2pjrB_
not modelled 99.9 58 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
23c1qhhD_
not modelled 99.9 58 PDB header:hydrolase
Chain: D: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
24c3dmnA_
not modelled 99.9 38 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative dna helicase;
PDBTitle: the crystal structure of the c-terminal domain of a possilbe dna2 helicase from lactobacillus plantarun wcfs1
25d1w36d1
not modelled 99.7 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
26d1w36d2
not modelled 99.7 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
27c3b85A_
not modelled 99.6 25 PDB header:hydrolase
Chain: A: PDB Molecule:phosphate starvation-inducible protein;
PDBTitle: crystal structure of predicted phosphate starvation-induced atpase2 phoh2 from corynebacterium glutamicum
28c3i5yA_
not modelled 98.7 15 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase mss116;
PDBTitle: structure of mss116p bound to ssrna containing a single 5-bru and amp-2 pnp
29c1qhhC_
not modelled 98.6 31 PDB header:hydrolase
Chain: C: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
30c2va8A_
not modelled 98.5 22 PDB header:hydrolase
Chain: A: PDB Molecule:ski2-type helicase;
PDBTitle: dna repair helicase hel308
31c2zj2A_
not modelled 98.4 16 PDB header:hydrolase
Chain: A: PDB Molecule:putative ski2-type helicase;
PDBTitle: archaeal dna helicase hjm apo state in form 1
32c2xgjA_
not modelled 98.4 24 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase dob1;
PDBTitle: structure of mtr4, a dexh helicase involved in nuclear rna2 processing and surveillance
33c3l9oA_
not modelled 98.4 24 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dob1;
PDBTitle: crystal structure of mtr4, a co-factor of the nuclear exosome
34d1gkub1
not modelled 98.4 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Helicase-like "domain" of reverse gyrase
35c1gm5A_
not modelled 98.4 19 PDB header:helicase
Chain: A: PDB Molecule:recg;
PDBTitle: structure of recg bound to three-way dna junction
36c4a4zA_
not modelled 98.3 22 PDB header:hydrolase
Chain: A: PDB Molecule:antiviral helicase ski2;
PDBTitle: crystal structure of the s. cerevisiae dexh helicase ski2 bound to2 amppnp
37c3oiyB_
not modelled 98.3 19 PDB header:isomerase
Chain: B: PDB Molecule:reverse gyrase helicase domain;
PDBTitle: helicase domain of reverse gyrase from thermotoga maritima
38c2z0mA_
not modelled 98.3 17 PDB header:rna binding protein
Chain: A: PDB Molecule:337aa long hypothetical atp-dependent rna
PDBTitle: crystal structure of hypothetical atp-dependent rna2 helicase from sulfolobus tokodaii
39c2db3D_
not modelled 98.3 17 PDB header:hydrolase/rna
Chain: D: PDB Molecule:atp-dependent rna helicase vasa;
PDBTitle: structural basis for rna unwinding by the dead-box protein2 drosophila vasa
40c2wv9A_
not modelled 98.3 18 PDB header:hydrolase
Chain: A: PDB Molecule:flavivirin protease ns2b regulatory subunit, flavivirin
PDBTitle: crystal structure of the ns3 protease-helicase from murray2 valley encephalitis virus
41c2hxyC_
not modelled 98.2 11 PDB header:hydrolase
Chain: C: PDB Molecule:probable atp-dependent rna helicase ddx48;
PDBTitle: crystal structure of human apo-eif4aiii
42c3dkpA_
not modelled 98.2 17 PDB header:hydrolase
Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx52;
PDBTitle: human dead-box rna-helicase ddx52, conserved domain i in complex with2 adp
43d1gl9b1
not modelled 98.2 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Helicase-like "domain" of reverse gyrase
44c2p6uA_
not modelled 98.2 19 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
45c3tbkA_
not modelled 98.2 14 PDB header:hydrolase
Chain: A: PDB Molecule:rig-i helicase domain;
PDBTitle: mouse rig-i atpase domain
46c1xtkA_
not modelled 98.2 19 PDB header:gene regulation
Chain: A: PDB Molecule:probable atp-dependent rna helicase p47;
PDBTitle: structure of decd to dead mutation of human uap56
47c1s2mA_
not modelled 98.2 20 PDB header:rna binding protein
Chain: A: PDB Molecule:putative atp-dependent rna helicase dhh1;
PDBTitle: crystal structure of the dead box protein dhh1p
48c2eyqA_
not modelled 98.1 16 PDB header:hydrolase
Chain: A: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor
49c2vbcA_
not modelled 98.1 17 PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus
50c1wp9D_
not modelled 98.1 15 PDB header:hydrolase
Chain: D: PDB Molecule:atp-dependent rna helicase, putative;
PDBTitle: crystal structure of pyrococcus furiosus hef helicase domain
51c2ocaA_
not modelled 98.1 10 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase uvsw;
PDBTitle: the crystal structure of t4 uvsw
52c1gl9B_
not modelled 98.1 12 PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp
53c3tmiA_
not modelled 98.1 12 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase ddx58;
PDBTitle: structural basis for rna recognition and activation of rig-i
54d2eyqa3
not modelled 98.0 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
55c2l8bA_
not modelled 98.0 14 PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: trai (381-569)
56c3pexA_
not modelled 98.0 15 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dbp5;
PDBTitle: s. cerevisiae dbp5 l327v bound to gle1 h337r and ip6
57d1rifa_
not modelled 98.0 10 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:DNA helicase UvsW
58d1wp9a1
not modelled 98.0 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
59c3fhtA_
not modelled 98.0 22 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase ddx19b;
PDBTitle: crystal structure of human dbp5 in complex with amppnp and rna
60c1ymfA_
not modelled 98.0 17 PDB header:hydrolase
Chain: A: PDB Molecule:genome polyprotein [contains: flavivirin
PDBTitle: crystal structure of yellow fever virus ns3 helicase2 complexed with adp
61c3ewsA_
not modelled 98.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx19b;
PDBTitle: human dead-box rna-helicase ddx19 in complex with adp
62d1c4oa1
not modelled 98.0 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
63c3kx2A_
not modelled 98.0 14 PDB header:hydrolase
Chain: A: PDB Molecule:pre-mrna-splicing factor atp-dependent rna
PDBTitle: crystal structure of prp43p in complex with adp
64c3bxzA_
not modelled 97.9 15 PDB header:transport protein
Chain: A: PDB Molecule:preprotein translocase subunit seca;
PDBTitle: crystal structure of the isolated dead motor domains from2 escherichia coli seca
65c2fwrA_
not modelled 97.9 28 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad25;
PDBTitle: structure of archaeoglobus fulgidis xpb
66c2jlrA_
not modelled 97.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:serine protease subunit ns3;
PDBTitle: dengue virus 4 ns3 helicase in complex with amppnp
67c1hv8B_
not modelled 97.9 21 PDB header:rna binding protein
Chain: B: PDB Molecule:putative atp-dependent rna helicase mj0669;
PDBTitle: crystal structure of a dead box protein from the2 hyperthermophile methanococcus jannaschii
68c3ly5A_
not modelled 97.9 18 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx18;
PDBTitle: ddx18 dead-domain
69c3llmB_
not modelled 97.9 16 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase a;
PDBTitle: crystal structure analysis of a rna helicase
70c2kbeA_
not modelled 97.9 15 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dbp5;
PDBTitle: solution structure of amino-terminal domain of dbp5p
71d2p6ra3
not modelled 97.9 25 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
72c2vsxA_
not modelled 97.8 15 PDB header:translation/hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase eif4a;
PDBTitle: crystal structure of a translation initiation complex
73c2qeqA_
not modelled 97.8 25 PDB header:hydrolase
Chain: A: PDB Molecule:flavivirin protease ns3 catalytic subunit;
PDBTitle: crystal structure of kunjin virus ns3 helicase
74c2pl3A_
not modelled 97.8 15 PDB header:hydrolase
Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx10;
PDBTitle: human dead-box rna helicase ddx10, dead domain in complex with adp
75c3b6eA_
not modelled 97.8 19 PDB header:hydrolase
Chain: A: PDB Molecule:interferon-induced helicase c domain-containing protein 1;
PDBTitle: crystal structure of human dech-box rna helicase mda5 (melanoma2 differentiation-associated protein 5), dech-domain
76c1c4oA_
not modelled 97.8 22 PDB header:replication
Chain: A: PDB Molecule:dna nucleotide excision repair enzyme uvrb;
PDBTitle: crystal structure of the dna nucleotide excision repair enzyme uvrb2 from thermus thermophilus
77c1a1vA_
not modelled 97.7 19 PDB header:hydrolase/dna
Chain: A: PDB Molecule:protein (ns3 protein);
PDBTitle: hepatitis c virus ns3 helicase domain complexed with single2 stranded sdna
78c1oywA_
not modelled 97.7 17 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase;
PDBTitle: structure of the recq catalytic core
79c2v1xB_
not modelled 97.7 17 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent dna helicase q1;
PDBTitle: crystal structure of human recq-like dna helicase
80c3fe2B_
not modelled 97.7 12 PDB header:hydrolase
Chain: B: PDB Molecule:probable atp-dependent rna helicase ddx5;
PDBTitle: human dead-box rna helicase ddx5 (p68), conserved domain i in complex2 with adp
81c3crw1_
not modelled 97.7 17 PDB header:hydrolase
Chain: 1: PDB Molecule:xpd/rad3 related dna helicase;
PDBTitle: "xpd_apo"
82c3iuyB_
not modelled 97.7 16 PDB header:hydrolase
Chain: B: PDB Molecule:probable atp-dependent rna helicase ddx53;
PDBTitle: crystal structure of ddx53 dead-box domain
83d1q0ua_
not modelled 97.7 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
84c2v6jA_
not modelled 97.7 14 PDB header:hydrolase
Chain: A: PDB Molecule:rna helicase;
PDBTitle: kokobera virus helicase: mutant met47thr
85d1gm5a3
not modelled 97.7 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
86c2vl7A_
not modelled 97.6 25 PDB header:unknown function
Chain: A: PDB Molecule:xpd;
PDBTitle: structure of s. tokodaii xpd4
87d1s2ma1
not modelled 97.6 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
88c2f55C_
not modelled 97.6 20 PDB header:hydrolase/dna
Chain: C: PDB Molecule:polyprotein;
PDBTitle: two hepatitis c virus ns3 helicase domains complexed with2 the same strand of dna
89c2d7dA_
not modelled 97.6 17 PDB header:hydrolase/dna
Chain: A: PDB Molecule:uvrabc system protein b;
PDBTitle: structural insights into the cryptic dna dependent atp-ase2 activity of uvrb
90d2fwra2
not modelled 97.6 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
91c1xx6B_
not modelled 97.5 26 PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: x-ray structure of clostridium acetobutylicum thymidine kinase with2 adp. northeast structural genomics target car26.
92c2z83A_
not modelled 97.5 25 PDB header:viral protein
Chain: A: PDB Molecule:helicase/nucleoside triphosphatase;
PDBTitle: crystal structure of catalytic domain of japanese2 encephalitis virus ns3 helicase/nucleoside triphosphatase3 at a resolution 1.8
93c1cu1B_
not modelled 97.5 19 PDB header:hydrolase
Chain: B: PDB Molecule:protein (protease/helicase ns3);
PDBTitle: crystal structure of an enzyme complex from hepatitis c2 virus
94d1oywa2
not modelled 97.5 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
95c2w74B_
not modelled 97.5 18 PDB header:hydrolase
Chain: B: PDB Molecule:type i restriction enzyme ecor124ii r protein;
PDBTitle: mutant (k220r) of the hsdr subunit of the ecor124i2 restriction enzyme in complex with atp
96c2oxcA_
not modelled 97.5 18 PDB header:hydrolase
Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx20;
PDBTitle: human dead-box rna helicase ddx20, dead domain in complex2 with adp
97c2gxqA_
not modelled 97.5 20 PDB header:hydrolase
Chain: A: PDB Molecule:heat resistant rna dependent atpase;
PDBTitle: hera n-terminal domain in complex with amp, crystal form 1
98c2cnwF_
not modelled 97.4 16 PDB header:signal recognition
Chain: F: PDB Molecule:cell division protein ftsy;
PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy
99d1a1va1
not modelled 97.4 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
100d1t6na_
not modelled 97.4 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
101d1qdea_
not modelled 97.4 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
102c3jvvA_
not modelled 97.4 22 PDB header:atp binding protein
Chain: A: PDB Molecule:twitching mobility protein;
PDBTitle: crystal structure of p. aeruginosa pilt with bound amp-pcp
103c2yhsA_
not modelled 97.4 20 PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the e. coli srp receptor ftsy
104d2bmfa2
not modelled 97.4 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
105c3h1tA_
not modelled 97.3 22 PDB header:hydrolase
Chain: A: PDB Molecule:type i site-specific restriction-modification
PDBTitle: the fragment structure of a putative hsdr subunit of a type2 i restriction enzyme from vibrio vulnificus yj016
106c3dmdA_
not modelled 97.3 22 PDB header:transport protein
Chain: A: PDB Molecule:signal recognition particle receptor;
PDBTitle: structures and conformations in solution of the signal recognition2 particle receptor from the archaeon pyrococcus furiosus
107d1wrba1
not modelled 97.3 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
108c2w00B_
not modelled 97.3 18 PDB header:hydrolase
Chain: B: PDB Molecule:hsdr;
PDBTitle: crystal structure of the hsdr subunit of the ecor124i2 restriction enzyme in complex with atp
109d2j0sa1
not modelled 97.3 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
110c2iy3A_
not modelled 97.3 20 PDB header:rna-binding
Chain: A: PDB Molecule:signal recognition particle protein ffh;
PDBTitle: structure of the e. coli signal recognition particle2 bound to a translating ribosome
111c3berA_
not modelled 97.3 22 PDB header:hydrolase
Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx47;
PDBTitle: human dead-box rna-helicase ddx47, conserved domain i in complex with2 amp
112d2fz4a1
not modelled 97.3 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
113c3fmoB_
not modelled 97.3 17 PDB header:oncoprotein/hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase ddx19b;
PDBTitle: crystal structure of the nucleoporin nup214 in complex with the dead-2 box helicase ddx19
114c1zu4A_
not modelled 97.3 13 PDB header:protein transport
Chain: A: PDB Molecule:ftsy;
PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212
115c3b9qA_
not modelled 97.2 18 PDB header:protein transport
Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit
PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana
116c3ezkB_
not modelled 97.2 19 PDB header:hydrolase
Chain: B: PDB Molecule:dna packaging protein gp17;
PDBTitle: bacteriophage t4 gp17 motor assembly based on crystal2 structures and cryo-em reconstructions
117c3fhcB_
not modelled 97.2 17 PDB header:transport protein/hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase ddx19b;
PDBTitle: crystal structure of human dbp5 in complex with nup214
118c2j7pA_
not modelled 97.2 22 PDB header:signal recognition
Chain: A: PDB Molecule:signal recognition particle protein;
PDBTitle: gmppnp-stabilized ng domain complex of the srp gtpases ffh2 and ftsy
119d1hv8a1
not modelled 97.2 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
120c2og2A_
not modelled 97.2 19 PDB header:protein transport
Chain: A: PDB Molecule:putative signal recognition particle receptor;
PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana

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


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
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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