Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP04993
DateThu Jan 5 10:58:32 GMT 2012
Unique Job IDb41bbb4cf7341fa9

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1w36G_
Top template information
PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex
Confidence and coverage
Confidence:100.0% Coverage: 88%
538 residues ( 88% 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  MKLQKQLLEAVEHKQLRPLDVQFALTVAGDEHPAVTLAAALLSHDAGEGHVCLPLSRLEN
Secondary structure 














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Disorder  ??























?

?





























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   .........70.........80.........90.........100.........110.........120
Sequence  NEASHPLLATCVSEIGELQNWEECLLASQAVSRGDEPTPMILCGDRLYLNRMWCNERTVA
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Disorder 



???????????











???????

























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   .........130.........140.........150.........160.........170.........180
Sequence  RFFNEVNHAIEVDEALLAQTLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTT
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Disorder 





???????













???





























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   .........190.........200.........210.........220.........230.........240
Sequence  VAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTL
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???
?
?????????????





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   .........250.........260.........270.........280.........290.........300
Sequence  HRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRDQ
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Disorder 






??????????










































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   .........310.........320.........330.........340.........350.........360
Sequence  LASVEAGAVLGDICAYANAGFTAERARQLSRLTGTHVPAGTGTEAASLRDSLCLLQKSYR
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Disorder 

















??

?









???
???
????














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   .........370.........380.........390.........400.........410.........420
Sequence  FGSDSGIGQLAAAINRGDKTAVKTVFQQDFTDIEKRLLQSGEDYIAMLEEALAGYGRYLD
Secondary structure 















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Disorder 
??
























































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   .........430.........440.........450.........460.........470.........480
Sequence  LLQARAEPDLIIQAFNEYQLLCALREGPFGVAGLNERIEQFMQQKRKIHRHPHSRWYEGR
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?????
?







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   .........490.........500.........510.........520.........530.........540
Sequence  PVMIARNDSALGLFNGDIGIALDRGQGTRVWFAMPDGNIKSVQPSRLPEHETTWAMTVHK
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   .........550.........560.........570.........580.........590.........600
Sequence  SQGSEFDHAALILPSQRTPVVTRELVYTAVTRARRRLSLYADERILSAAIATRTERRSGL
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?
?































???????
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   ........
Sequence  AALFSSRE
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 1w36 chain G

3D model

Region: 2 - 606
Aligned: 538
Modelled: 549
Confidence: 100.0%
Identity: 100%
PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex

Phyre2

PDB 3e1s chain A

3D model

Region: 8 - 606
Aligned: 504
Modelled: 525
Confidence: 100.0%
Identity: 30%
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2

Phyre2

PDB 1w36 chain D domain 1

3D model

Region: 2 - 360
Aligned: 348
Modelled: 359
Confidence: 100.0%
Identity: 100%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 2wjy chain A

3D model

Region: 148 - 586
Aligned: 336
Modelled: 347
Confidence: 100.0%
Identity: 22%
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 2xzl chain A

3D model

Region: 149 - 588
Aligned: 348
Modelled: 357
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex

Phyre2

PDB 2gk7 chain A

3D model

Region: 149 - 586
Aligned: 346
Modelled: 357
Confidence: 100.0%
Identity: 21%
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 2is6 chain B

3D model

Region: 149 - 582
Aligned: 377
Modelled: 394
Confidence: 100.0%
Identity: 25%
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: 149 - 581
Aligned: 402
Modelled: 406
Confidence: 100.0%
Identity: 21%
PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (atp-dependent dna helicase rep.);
PDBTitle: e. coli rep helicase/dna complex

Phyre2

PDB 1w36 chain D domain 2

3D model

Region: 361 - 606
Aligned: 190
Modelled: 190
Confidence: 100.0%
Identity: 100%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1pjr chain A

3D model

Region: 148 - 582
Aligned: 395
Modelled: 408
Confidence: 100.0%
Identity: 20%
PDB header:helicase
Chain: A: PDB Molecule:pcra;
PDBTitle: structure of dna helicase

Phyre2

PDB 3lfu chain A

3D model

Region: 148 - 582
Aligned: 404
Modelled: 408
Confidence: 100.0%
Identity: 24%
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: 164 - 582
Aligned: 358
Modelled: 360
Confidence: 99.9%
Identity: 29%
PDB header:recombination
Chain: E: PDB Molecule:exodeoxyribonuclease v beta chain;
PDBTitle: recbcd:dna complex

Phyre2

PDB 2l8b chain A

3D model

Region: 145 - 312
Aligned: 139
Modelled: 151
Confidence: 99.9%
Identity: 17%
PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: trai (381-569)

Phyre2

PDB 3b85 chain A

3D model

Region: 149 - 303
Aligned: 137
Modelled: 139
Confidence: 99.9%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:phosphate starvation-inducible protein;
PDBTitle: crystal structure of predicted phosphate starvation-induced atpase2 phoh2 from corynebacterium glutamicum

Phyre2

PDB 1uaa chain A domain 1

3D model

Region: 149 - 391
Aligned: 212
Modelled: 216
Confidence: 99.9%
Identity: 28%
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 1

3D model

Region: 148 - 393
Aligned: 215
Modelled: 219
Confidence: 99.9%
Identity: 22%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 2pjr chain F

3D model

Region: 148 - 419
Aligned: 241
Modelled: 245
Confidence: 99.9%
Identity: 22%
PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex

Phyre2

PDB 1w36 chain B domain 1

3D model

Region: 164 - 382
Aligned: 188
Modelled: 190
Confidence: 99.8%
Identity: 32%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1qhh chain A

3D model

Region: 148 - 254
Aligned: 105
Modelled: 107
Confidence: 99.5%
Identity: 19%
PDB header:hydrolase
Chain: A: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp

Phyre2

PDB 3dmn chain A

3D model

Region: 533 - 582
Aligned: 50
Modelled: 50
Confidence: 99.4%
Identity: 26%
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

Phyre2
1

c1w36G_
2

c3e1sA_
3

d1w36d1
4

c2wjyA_
5

c2xzlA_
6

c2gk7A_
7

c2is6B_
8

c1uaaB_
9

d1w36d2
10

c1pjrA_
11

c3lfuA_
12

c1w36E_
13

c2l8bA_
14

c3b85A_
15

d1uaaa1
16

d1pjra1
17

c2pjrF_
18

d1w36b1
19

c1qhhA_
20

c3dmnA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1w36G_



100.0 100 PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex
2c3e1sA_



100.0 30 PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2
3d1w36d1



100.0 100 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
4c2wjyA_



100.0 22 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
5c2xzlA_



100.0 22 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex
6c2gk7A_



100.0 21 PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: structural and functional insights into the human upf1 helicase core
7c2is6B_



100.0 25 PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex
8c1uaaB_



100.0 21 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (atp-dependent dna helicase rep.);
PDBTitle: e. coli rep helicase/dna complex
9d1w36d2



100.0 100 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
10c1pjrA_



100.0 20 PDB header:helicase
Chain: A: PDB Molecule:pcra;
PDBTitle: structure of dna helicase
11c3lfuA_



100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of e. coli uvrd
12c1w36E_



99.9 29 PDB header:recombination
Chain: E: PDB Molecule:exodeoxyribonuclease v beta chain;
PDBTitle: recbcd:dna complex
13c2l8bA_



99.9 17 PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: trai (381-569)
14c3b85A_



99.9 22 PDB header:hydrolase
Chain: A: PDB Molecule:phosphate starvation-inducible protein;
PDBTitle: crystal structure of predicted phosphate starvation-induced atpase2 phoh2 from corynebacterium glutamicum
15d1uaaa1



99.9 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
16d1pjra1



99.9 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
17c2pjrF_



99.9 22 PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
18d1w36b1



99.8 32 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
19c1qhhA_



99.5 19 PDB header:hydrolase
Chain: A: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
20c3dmnA_



99.4 26 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
21d1w36b2



not modelled 99.4 32 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
22c2pjrB_



not modelled 99.3 31 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
23c1qhhD_



not modelled 99.2 33 PDB header:hydrolase
Chain: D: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
24d1pjra2



not modelled 99.2 30 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
25d1uaaa2



not modelled 99.1 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
26c2xgjA_



not modelled 98.9 18 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
27c2wv9A_



not modelled 98.9 25 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
28c2vbcA_



not modelled 98.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus
29c2eyqA_



not modelled 98.8 18 PDB header:hydrolase
Chain: A: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor
30d1gkub1



not modelled 98.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Helicase-like "domain" of reverse gyrase
31d1rifa_



not modelled 98.8 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:DNA helicase UvsW
32d2eyqa3



not modelled 98.8 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
33c1gm5A_



not modelled 98.8 14 PDB header:helicase
Chain: A: PDB Molecule:recg;
PDBTitle: structure of recg bound to three-way dna junction
34c2zj2A_



not modelled 98.8 16 PDB header:hydrolase
Chain: A: PDB Molecule:putative ski2-type helicase;
PDBTitle: archaeal dna helicase hjm apo state in form 1
35c3l9oA_



not modelled 98.8 17 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dob1;
PDBTitle: crystal structure of mtr4, a co-factor of the nuclear exosome
36c2ocaA_



not modelled 98.8 13 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase uvsw;
PDBTitle: the crystal structure of t4 uvsw
37d2fwra2



not modelled 98.7 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
38c3oiyB_



not modelled 98.7 16 PDB header:isomerase
Chain: B: PDB Molecule:reverse gyrase helicase domain;
PDBTitle: helicase domain of reverse gyrase from thermotoga maritima
39d2fz4a1



not modelled 98.7 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
40c3kx2A_



not modelled 98.7 16 PDB header:hydrolase
Chain: A: PDB Molecule:pre-mrna-splicing factor atp-dependent rna
PDBTitle: crystal structure of prp43p in complex with adp
41c2ja1A_



not modelled 98.7 21 PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from b. cereus with ttp bound as phosphate2 donor.
42c3llmB_



not modelled 98.7 17 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase a;
PDBTitle: crystal structure analysis of a rna helicase
43d1gl9b1



not modelled 98.7 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Helicase-like "domain" of reverse gyrase
44c2va8A_



not modelled 98.6 13 PDB header:hydrolase
Chain: A: PDB Molecule:ski2-type helicase;
PDBTitle: dna repair helicase hel308
45c3ezkB_



not modelled 98.6 16 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
46c2iy3A_



not modelled 98.6 23 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
47c4a4zA_



not modelled 98.6 17 PDB header:hydrolase
Chain: A: PDB Molecule:antiviral helicase ski2;
PDBTitle: crystal structure of the s. cerevisiae dexh helicase ski2 bound to2 amppnp
48c2cnwF_



not modelled 98.6 23 PDB header:signal recognition
Chain: F: PDB Molecule:cell division protein ftsy;
PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy
49d1hv8a1



not modelled 98.6 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
50c2p6uA_



not modelled 98.6 17 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
51c2fwrA_



not modelled 98.6 16 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad25;
PDBTitle: structure of archaeoglobus fulgidis xpb
52c3dkpA_



not modelled 98.6 16 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
53c2jlrA_



not modelled 98.6 24 PDB header:hydrolase
Chain: A: PDB Molecule:serine protease subunit ns3;
PDBTitle: dengue virus 4 ns3 helicase in complex with amppnp
54d1a1va1



not modelled 98.6 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
55c2j37W_



not modelled 98.6 13 PDB header:ribosome
Chain: W: PDB Molecule:signal recognition particle 54 kda protein
PDBTitle: model of mammalian srp bound to 80s rncs
56c1vmaA_



not modelled 98.6 19 PDB header:protein transport
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: crystal structure of cell division protein ftsy (tm0570) from2 thermotoga maritima at 1.60 a resolution
57d1gm5a3



not modelled 98.6 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
58d2p6ra3



not modelled 98.6 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
59c3b6eA_



not modelled 98.6 11 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
60c3tbkA_



not modelled 98.5 12 PDB header:hydrolase
Chain: A: PDB Molecule:rig-i helicase domain;
PDBTitle: mouse rig-i atpase domain
61c1gl9B_



not modelled 98.5 18 PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp
62c2z83A_



not modelled 98.5 26 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
63c1sxjD_



not modelled 98.5 17 PDB header:replication
Chain: D: PDB Molecule:activator 1 41 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
64c3tmiA_



not modelled 98.5 14 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase ddx58;
PDBTitle: structural basis for rna recognition and activation of rig-i
65d1q0ua_



not modelled 98.5 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
66c3ly5A_



not modelled 98.5 16 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx18;
PDBTitle: ddx18 dead-domain
67c2v6jA_



not modelled 98.5 27 PDB header:hydrolase
Chain: A: PDB Molecule:rna helicase;
PDBTitle: kokobera virus helicase: mutant met47thr
68c3dm5A_



not modelled 98.4 21 PDB header:rna binding protein, transport protein
Chain: A: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: structures of srp54 and srp19, the two proteins assembling2 the ribonucleic core of the signal recognition particle3 from the archaeon pyrococcus furiosus.
69c2og2A_



not modelled 98.4 22 PDB header:protein transport
Chain: A: PDB Molecule:putative signal recognition particle receptor;
PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana
70c1ymfA_



not modelled 98.4 19 PDB header:hydrolase
Chain: A: PDB Molecule:genome polyprotein [contains: flavivirin
PDBTitle: crystal structure of yellow fever virus ns3 helicase2 complexed with adp
71c2j7pA_



not modelled 98.4 26 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
72c3b9qA_



not modelled 98.4 22 PDB header:protein transport
Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit
PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana
73c2o0hA_



not modelled 98.4 15 PDB header:hydrolase
Chain: A: PDB Molecule:dna packaging protein gp17;
PDBTitle: t4 gp17 atpase domain mutant complexed with atp
74c1zu4A_



not modelled 98.4 20 PDB header:protein transport
Chain: A: PDB Molecule:ftsy;
PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212
75d1z3ix2



not modelled 98.4 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
76c2qeqA_



not modelled 98.4 25 PDB header:hydrolase
Chain: A: PDB Molecule:flavivirin protease ns3 catalytic subunit;
PDBTitle: crystal structure of kunjin virus ns3 helicase
77c3dmdA_



not modelled 98.4 24 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
78c3pfiB_



not modelled 98.4 26 PDB header:hydrolase
Chain: B: PDB Molecule:holliday junction atp-dependent dna helicase ruvb;
PDBTitle: 2.7 angstrom resolution crystal structure of a probable holliday2 junction dna helicase (ruvb) from campylobacter jejuni subsp. jejuni3 nctc 11168 in complex with adenosine-5'-diphosphate
79d1wp9a1



not modelled 98.4 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
80c3te6A_



not modelled 98.4 6 PDB header:gene regulation
Chain: A: PDB Molecule:regulatory protein sir3;
PDBTitle: crystal structure of the s. cerevisiae sir3 aaa+ domain
81c2gxqA_



not modelled 98.4 18 PDB header:hydrolase
Chain: A: PDB Molecule:heat resistant rna dependent atpase;
PDBTitle: hera n-terminal domain in complex with amp, crystal form 1
82c2yhsA_



not modelled 98.3 25 PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the e. coli srp receptor ftsy
83c1cu1B_



not modelled 98.3 17 PDB header:hydrolase
Chain: B: PDB Molecule:protein (protease/helicase ns3);
PDBTitle: crystal structure of an enzyme complex from hepatitis c2 virus
84c2pl3A_



not modelled 98.3 20 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
85d1s2ma1



not modelled 98.3 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
86d1veca_



not modelled 98.3 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
87c2qy9A_



not modelled 98.3 25 PDB header:protein transport
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the ng+1 construct of the e. coli srp receptor2 ftsy
88c3berA_



not modelled 98.3 18 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
89c3fe2B_



not modelled 98.3 19 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
90c3i5yA_



not modelled 98.3 19 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
91c3ec2A_



not modelled 98.3 19 PDB header:replication
Chain: A: PDB Molecule:dna replication protein dnac;
PDBTitle: crystal structure of the dnac helicase loader
92d1yksa1



not modelled 98.2 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
93c1iqpF_



not modelled 98.2 18 PDB header:replication
Chain: F: PDB Molecule:rfcs;
PDBTitle: crystal structure of the clamp loader small subunit from2 pyrococcus furiosus
94c2db3D_



not modelled 98.2 16 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
95c1wp9D_



not modelled 98.2 17 PDB header:hydrolase
Chain: D: PDB Molecule:atp-dependent rna helicase, putative;
PDBTitle: crystal structure of pyrococcus furiosus hef helicase domain
96d1qdea_



not modelled 98.2 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
97c2oxcA_



not modelled 98.2 17 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
98c3iuyB_



not modelled 98.2 18 PDB header:hydrolase
Chain: B: PDB Molecule:probable atp-dependent rna helicase ddx53;
PDBTitle: crystal structure of ddx53 dead-box domain
99d1fnna2



not modelled 98.2 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
100c1sxjC_



not modelled 98.2 17 PDB header:replication
Chain: C: PDB Molecule:activator 1 40 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
101c1z63A_



not modelled 98.2 14 PDB header:hydrolase/dna complex
Chain: A: PDB Molecule:helicase of the snf2/rad54 hamily;
PDBTitle: sulfolobus solfataricus swi2/snf2 atpase core in complex2 with dsdna
102c3u5zM_



not modelled 98.2 19 PDB header:dna binding protein/dna
Chain: M: PDB Molecule:dna polymerase accessory protein 44;
PDBTitle: structure of t4 bacteriophage clamp loader bound to the t4 clamp,2 primer-template dna, and atp analog
103c1oywA_



not modelled 98.2 17 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase;
PDBTitle: structure of the recq catalytic core
104d1oywa2



not modelled 98.2 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
105c2f55C_



not modelled 98.2 23 PDB header:hydrolase/dna
Chain: C: PDB Molecule:polyprotein;
PDBTitle: two hepatitis c virus ns3 helicase domains complexed with2 the same strand of dna
106d2j0sa1



not modelled 98.2 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
107c2kbeA_



not modelled 98.2 15 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dbp5;
PDBTitle: solution structure of amino-terminal domain of dbp5p
108c1a1vA_



not modelled 98.2 22 PDB header:hydrolase/dna
Chain: A: PDB Molecule:protein (ns3 protein);
PDBTitle: hepatitis c virus ns3 helicase domain complexed with single2 stranded sdna
109c2z0mA_



not modelled 98.2 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
110c1z3iX_



not modelled 98.1 13 PDB header:recombination/dna binding
Chain: X: PDB Molecule:similar to rad54-like;
PDBTitle: structure of the swi2/snf2 chromatin remodeling domain of eukaryotic2 rad54
111c2r44A_



not modelled 98.1 16 PDB header:hydrolase
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a putative atpase (chu_0153) from cytophaga2 hutchinsonii atcc 33406 at 2.00 a resolution
112c2chgB_



not modelled 98.1 20 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
113c1s2mA_



not modelled 98.1 16 PDB header:rna binding protein
Chain: A: PDB Molecule:putative atp-dependent rna helicase dhh1;
PDBTitle: crystal structure of the dead box protein dhh1p
114c3pvsA_



not modelled 98.1 22 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
115c2zpaB_



not modelled 98.1 23 PDB header:transferase
Chain: B: PDB Molecule:uncharacterized protein ypfi;
PDBTitle: crystal structure of trna(met) cytidine acetyltransferase
116c1hv8B_



not modelled 98.1 11 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
117c3mwyW_



not modelled 98.1 12 PDB header:hydrolase
Chain: W: PDB Molecule:chromo domain-containing protein 1;
PDBTitle: crystal structure of the chromodomain-atpase portion of the yeast chd12 chromatin remodeler
118c1in8A_



not modelled 98.1 26 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
119c1xx6B_



not modelled 98.1 21 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.
120c2vl7A_



not modelled 98.1 18 PDB header:unknown function
Chain: A: PDB Molecule:xpd;
PDBTitle: structure of s. tokodaii xpd4

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
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