Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP14565
DateWed Jan 25 15:20:38 GMT 2012
Unique Job IDec7a67129bc5f945

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1p4da_
Top template information
Fold:Origin of replication-binding domain, RBD-like
Superfamily:Origin of replication-binding domain, RBD-like
Family:Relaxase domain
Confidence and coverage
Confidence:100.0% Coverage: 15%
264 residues ( 15% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
1141 residues ( 65%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRL
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Disorder  ???????????

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   .........70.........80.........90.........100.........110.........120
Sequence  PDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEAL
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   .........130.........140.........150.........160.........170.........180
Sequence  ASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKV
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   .........190.........200.........210.........220.........230.........240
Sequence  GKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQT
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   .........250.........260.........270.........280.........290.........300
Sequence  IREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD
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   .........310.........320.........330.........340.........350.........360
Sequence  LRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPENGVIERARAG
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   .........370.........380.........390.........400.........410.........420
Sequence  IDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
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   .........430.........440.........450.........460.........470.........480
Sequence  DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDE
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   .........490.........500.........510.........520.........530.........540
Sequence  RLSGELITGRRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQR
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   .........550.........560.........570.........580.........590.........600
Sequence  TGTGSALMAMKDAGVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQ
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   .........610.........620.........630.........640.........650.........660
Sequence  VSGVREQAILTQAIRSELKTQGVLGLPEVTMTALSPVWLDSRSRYLRDMYRPGMVMEQWN
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   .........670.........680.........690.........700.........710.........720
Sequence  PETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRV
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   .........730.........740.........750.........760.........770.........780
Sequence  TGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKLENGWVETPGH
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   .........790.........800.........810.........820.........830.........840
Sequence  SVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
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   .........850.........860.........870.........880.........890.........900
Sequence  KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTG
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   .........910.........920.........930.........940.........950.........960
Sequence  FTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMER
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   .........970.........980.........990.........1000.........1010.........1020
Sequence  VPGELMEKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRV
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   .........1030.........1040.........1050.........1060.........1070.........1080
Sequence  VGLGPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTDM
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   .........1090.........1100.........1110.........1120.........1130.........1140
Sequence  ARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAADVAIMKEIVRQTPELREAV
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   .........1150.........1160.........1170.........1180.........1190.........1200
Sequence  YSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEAQQKAMLKGEA
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   .........1210.........1220.........1230.........1240.........1250.........1260
Sequence  FPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
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   .........1270.........1280.........1290.........1300.........1310.........1320
Sequence  VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLIS
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   .........1330.........1340.........1350.........1360.........1370.........1380
Sequence  PREAVAEGVTLYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQT
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   .........1390.........1400.........1410.........1420.........1430.........1440
Sequence  REIRPGQEQAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMK
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   .........1450.........1460.........1470.........1480.........1490.........1500
Sequence  QHVQVYTDNRQGWTDAINNAVQKGTAHDVFEPKPDREVMNAERLFSTARELRDVAAGRAV
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   .........1510.........1520.........1530.........1540.........1550.........1560
Sequence  LRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAGIWLNPLTTDDGNGLRGFSGE
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   .........1570.........1580.........1590.........1600.........1610.........1620
Sequence  GRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGEGRPWNPGAIT
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   .........1630.........1640.........1650.........1660.........1670.........1680
Sequence  GGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
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   .........1690.........1700.........1710.........1720.........1730.........1740
Sequence  DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQME
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   .........1750......
Sequence  RDMVRDLQKEKTLGGD
Secondary structure 



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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 1p4d chain A

3D model

Region: 1 - 264
Aligned: 264
Modelled: 264
Confidence: 100.0%
Identity: 90%
Fold: Origin of replication-binding domain, RBD-like
Superfamily: Origin of replication-binding domain, RBD-like
Family: Relaxase domain

Phyre2

PDB 1omh chain A

3D model

Region: 3 - 288
Aligned: 266
Modelled: 276
Confidence: 100.0%
Identity: 38%
Fold: Origin of replication-binding domain, RBD-like
Superfamily: Origin of replication-binding domain, RBD-like
Family: Relaxase domain

Phyre2

PDB 3l6t chain B

3D model

Region: 22 - 227
Aligned: 190
Modelled: 206
Confidence: 100.0%
Identity: 41%
PDB header:hydrolase
Chain: B: PDB Molecule:mobilization protein trai;
PDBTitle: crystal structure of an n-terminal mutant of the plasmid pcu1 trai2 relaxase domain

Phyre2

PDB 3e1s chain A

3D model

Region: 864 - 1463
Aligned: 464
Modelled: 486
Confidence: 100.0%
Identity: 22%
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 G

3D model

Region: 838 - 1467
Aligned: 471
Modelled: 485
Confidence: 100.0%
Identity: 18%
PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex

Phyre2

PDB 2l8b chain A

3D model

Region: 381 - 568
Aligned: 188
Modelled: 188
Confidence: 100.0%
Identity: 100%
PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: trai (381-569)

Phyre2

PDB 1w36 chain D domain 1

3D model

Region: 837 - 1123
Aligned: 284
Modelled: 287
Confidence: 100.0%
Identity: 18%
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: 969 - 1448
Aligned: 322
Modelled: 340
Confidence: 100.0%
Identity: 20%
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: 969 - 1448
Aligned: 322
Modelled: 341
Confidence: 100.0%
Identity: 19%
PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex

Phyre2

PDB 2gk7 chain A

3D model

Region: 969 - 1448
Aligned: 322
Modelled: 341
Confidence: 100.0%
Identity: 20%
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: 965 - 1448
Aligned: 434
Modelled: 435
Confidence: 99.9%
Identity: 20%
PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex

Phyre2

PDB 3b85 chain A

3D model

Region: 968 - 1132
Aligned: 153
Modelled: 165
Confidence: 99.9%
Identity: 19%
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 1pjr chain A

3D model

Region: 961 - 1447
Aligned: 418
Modelled: 423
Confidence: 99.9%
Identity: 19%
PDB header:helicase
Chain: A: PDB Molecule:pcra;
PDBTitle: structure of dna helicase

Phyre2

PDB 1uaa chain B

3D model

Region: 969 - 1447
Aligned: 409
Modelled: 414
Confidence: 99.9%
Identity: 18%
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: 965 - 1447
Aligned: 447
Modelled: 452
Confidence: 99.8%
Identity: 17%
PDB header:hydrolase
Chain: A: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of e. coli uvrd

Phyre2

PDB 1pjr chain A domain 1

3D model

Region: 958 - 1147
Aligned: 185
Modelled: 190
Confidence: 99.7%
Identity: 23%
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: 961 - 1246
Aligned: 252
Modelled: 257
Confidence: 99.7%
Identity: 19%
PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex

Phyre2

PDB 3fld chain A

3D model

Region: 1476 - 1627
Aligned: 152
Modelled: 152
Confidence: 99.6%
Identity: 100%
PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: crystal structure of the trai c-terminal domain

Phyre2

PDB 1uaa chain A domain 1

3D model

Region: 969 - 1147
Aligned: 168
Modelled: 179
Confidence: 99.6%
Identity: 24%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1w36 chain D domain 2

3D model

Region: 1387 - 1468
Aligned: 79
Modelled: 82
Confidence: 99.5%
Identity: 18%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2
1

d1p4da_
2

d1omha_
3

c3l6tB_
4

c3e1sA_
5

c1w36G_
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c2l8bA_
7

d1w36d1
8

c2wjyA_
9

c2xzlA_
10

c2gk7A_
11

c2is6B_
12

c3b85A_
13

c1pjrA_
14

c1uaaB_
15

c3lfuA_
16

d1pjra1
17

c2pjrF_
18

c3fldA_
19

d1uaaa1
20

d1w36d2
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1p4da_



100.0 90 Fold:Origin of replication-binding domain, RBD-like
Superfamily:Origin of replication-binding domain, RBD-like
Family:Relaxase domain
2d1omha_



100.0 38 Fold:Origin of replication-binding domain, RBD-like
Superfamily:Origin of replication-binding domain, RBD-like
Family:Relaxase domain
3c3l6tB_



100.0 41 PDB header:hydrolase
Chain: B: PDB Molecule:mobilization protein trai;
PDBTitle: crystal structure of an n-terminal mutant of the plasmid pcu1 trai2 relaxase domain
4c3e1sA_



100.0 22 PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2
5c1w36G_



100.0 18 PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex
6c2l8bA_



100.0 100 PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: trai (381-569)
7d1w36d1



100.0 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
8c2wjyA_



100.0 20 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
9c2xzlA_



100.0 19 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex
10c2gk7A_



100.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: structural and functional insights into the human upf1 helicase core
11c2is6B_



99.9 20 PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex
12c3b85A_



99.9 19 PDB header:hydrolase
Chain: A: PDB Molecule:phosphate starvation-inducible protein;
PDBTitle: crystal structure of predicted phosphate starvation-induced atpase2 phoh2 from corynebacterium glutamicum
13c1pjrA_



99.9 19 PDB header:helicase
Chain: A: PDB Molecule:pcra;
PDBTitle: structure of dna helicase
14c1uaaB_



99.9 18 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (atp-dependent dna helicase rep.);
PDBTitle: e. coli rep helicase/dna complex
15c3lfuA_



99.8 17 PDB header:hydrolase
Chain: A: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of e. coli uvrd
16d1pjra1



99.7 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
17c2pjrF_



99.7 19 PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
18c3fldA_



99.6 100 PDB header:hydrolase
Chain: A: PDB Molecule:protein trai;
PDBTitle: crystal structure of the trai c-terminal domain
19d1uaaa1



99.6 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
20d1w36d2



99.5 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
21d1w36b1



not modelled 99.3 32 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
22c1qhhA_



not modelled 99.1 25 PDB header:hydrolase
Chain: A: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
23c1w36E_



not modelled 99.0 19 PDB header:recombination
Chain: E: PDB Molecule:exodeoxyribonuclease v beta chain;
PDBTitle: recbcd:dna complex
24c3dmnA_



not modelled 98.7 13 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
25c2vbcA_



not modelled 98.6 25 PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus
26d1w36b2



not modelled 98.4 35 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
27c2wv9A_



not modelled 98.3 24 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
28c2ja1A_



not modelled 98.3 12 PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from b. cereus with ttp bound as phosphate2 donor.
29c1qhhD_



not modelled 98.2 20 PDB header:hydrolase
Chain: D: PDB Molecule:protein (pcra (subunit));
PDBTitle: structure of dna helicase with adpnp
30c3dkpA_



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
31c2pjrB_



not modelled 98.2 20 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
32c3te6A_



not modelled 98.2 6 PDB header:gene regulation
Chain: A: PDB Molecule:regulatory protein sir3;
PDBTitle: crystal structure of the s. cerevisiae sir3 aaa+ domain
33c1sxjC_



not modelled 98.2 13 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)
34c1sxjD_



not modelled 98.1 11 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)
35c1sxjA_



not modelled 98.1 13 PDB header:replication
Chain: A: PDB Molecule:activator 1 95 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)
36c1gm5A_



not modelled 98.1 21 PDB header:helicase
Chain: A: PDB Molecule:recg;
PDBTitle: structure of recg bound to three-way dna junction
37d1pjra2



not modelled 98.0 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
38c3kx2A_



not modelled 98.0 16 PDB header:hydrolase
Chain: A: PDB Molecule:pre-mrna-splicing factor atp-dependent rna
PDBTitle: crystal structure of prp43p in complex with adp
39d1rifa_



not modelled 98.0 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:DNA helicase UvsW
40d1a1va1



not modelled 98.0 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
41d1uaaa2



not modelled 97.9 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
42c2z83A_



not modelled 97.9 22 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
43c1iqpF_



not modelled 97.9 16 PDB header:replication
Chain: F: PDB Molecule:rfcs;
PDBTitle: crystal structure of the clamp loader small subunit from2 pyrococcus furiosus
44c2hcbC_



not modelled 97.9 18 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
45c2kjqA_



not modelled 97.9 20 PDB header:replication
Chain: A: PDB Molecule:dnaa-related protein;
PDBTitle: solution structure of protein nmb1076 from neisseria meningitidis.2 northeast structural genomics consortium target mr101b.
46c2zpaB_



not modelled 97.9 12 PDB header:transferase
Chain: B: PDB Molecule:uncharacterized protein ypfi;
PDBTitle: crystal structure of trna(met) cytidine acetyltransferase
47c3llmB_



not modelled 97.9 14 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase a;
PDBTitle: crystal structure analysis of a rna helicase
48d1sxja2



not modelled 97.9 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
49c3ec2A_



not modelled 97.9 19 PDB header:replication
Chain: A: PDB Molecule:dna replication protein dnac;
PDBTitle: crystal structure of the dnac helicase loader
50c1cu1B_



not modelled 97.9 23 PDB header:hydrolase
Chain: B: PDB Molecule:protein (protease/helicase ns3);
PDBTitle: crystal structure of an enzyme complex from hepatitis c2 virus
51c3pvsA_



not modelled 97.9 23 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
52d1ny5a2



not modelled 97.9 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
53c2chgB_



not modelled 97.9 13 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
54c2jlrA_



not modelled 97.8 26 PDB header:hydrolase
Chain: A: PDB Molecule:serine protease subunit ns3;
PDBTitle: dengue virus 4 ns3 helicase in complex with amppnp
55d1gkub1



not modelled 97.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Helicase-like "domain" of reverse gyrase
56d2eyqa3



not modelled 97.8 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
57d1p9ra_



not modelled 97.8 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
58c3i5yA_



not modelled 97.8 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
59c2qgzA_



not modelled 97.8 13 PDB header:hydrolase
Chain: A: PDB Molecule:putative primosome component;
PDBTitle: crystal structure of a putative primosome component from2 streptococcus pyogenes serotype m3. northeast structural3 genomics target dr58
60d2fz4a1



not modelled 97.8 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
61d2fwra2



not modelled 97.8 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
62c2v6jA_



not modelled 97.8 27 PDB header:hydrolase
Chain: A: PDB Molecule:rna helicase;
PDBTitle: kokobera virus helicase: mutant met47thr
63c2p6uA_



not modelled 97.8 13 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
64d1iqpa2



not modelled 97.7 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
65c3pfiB_



not modelled 97.7 19 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
66d1fnna2



not modelled 97.7 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
67d1njfa_



not modelled 97.7 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
68c1ymfA_



not modelled 97.7 23 PDB header:hydrolase
Chain: A: PDB Molecule:genome polyprotein [contains: flavivirin
PDBTitle: crystal structure of yellow fever virus ns3 helicase2 complexed with adp
69c1a1vA_



not modelled 97.7 20 PDB header:hydrolase/dna
Chain: A: PDB Molecule:protein (ns3 protein);
PDBTitle: hepatitis c virus ns3 helicase domain complexed with single2 stranded sdna
70c3u5zM_



not modelled 97.7 16 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
71c3iuyB_



not modelled 97.7 18 PDB header:hydrolase
Chain: B: PDB Molecule:probable atp-dependent rna helicase ddx53;
PDBTitle: crystal structure of ddx53 dead-box domain
72c3b9qA_



not modelled 97.6 15 PDB header:protein transport
Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit
PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana
73c1xxhB_



not modelled 97.6 16 PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii subunit gamma;
PDBTitle: atpgs bound e. coli clamp loader complex
74c2r44A_



not modelled 97.6 9 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
75d1yksa1



not modelled 97.6 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
76c2qeqA_



not modelled 97.6 25 PDB header:hydrolase
Chain: A: PDB Molecule:flavivirin protease ns3 catalytic subunit;
PDBTitle: crystal structure of kunjin virus ns3 helicase
77c2cnwF_



not modelled 97.6 19 PDB header:signal recognition
Chain: F: PDB Molecule:cell division protein ftsy;
PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy
78c2chvE_



not modelled 97.6 15 PDB header:dna-binding protein
Chain: E: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c adpnp complex
79c2c99A_



not modelled 97.6 16 PDB header:transcription regulation
Chain: A: PDB Molecule:psp operon transcriptional activator;
PDBTitle: structural basis of the nucleotide driven conformational2 changes in the aaa domain of transcription activator pspf
80c2ocaA_



not modelled 97.6 12 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase uvsw;
PDBTitle: the crystal structure of t4 uvsw
81c3pxiB_



not modelled 97.6 18 PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc
82c2j7pA_



not modelled 97.5 18 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
83c1sxjB_



not modelled 97.5 12 PDB header:replication
Chain: B: PDB Molecule:activator 1 37 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)
84d1gm5a3



not modelled 97.5 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
85d1l8qa2



not modelled 97.5 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
86c3bosA_



not modelled 97.5 15 PDB header:hydrolase regulator,dna binding protein
Chain: A: PDB Molecule:putative dna replication factor;
PDBTitle: crystal structure of a putative dna replication regulator hda2 (sama_1916) from shewanella amazonensis sb2b at 1.75 a resolution
87c2fwrA_



not modelled 97.5 18 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad25;
PDBTitle: structure of archaeoglobus fulgidis xpb
88c2og2A_



not modelled 97.5 14 PDB header:protein transport
Chain: A: PDB Molecule:putative signal recognition particle receptor;
PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana
89c2va8A_



not modelled 97.5 17 PDB header:hydrolase
Chain: A: PDB Molecule:ski2-type helicase;
PDBTitle: dna repair helicase hel308
90c3jvvA_



not modelled 97.5 13 PDB header:atp binding protein
Chain: A: PDB Molecule:twitching mobility protein;
PDBTitle: crystal structure of p. aeruginosa pilt with bound amp-pcp
91d1hv8a1



not modelled 97.5 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
92d1sxjc2



not modelled 97.5 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
93c2xgjA_



not modelled 97.5 19 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
94c3ly5A_



not modelled 97.5 18 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx18;
PDBTitle: ddx18 dead-domain
95d1r6bx3



not modelled 97.5 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
96c1xx6B_



not modelled 97.5 14 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.
97d1um8a_



not modelled 97.5 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
98c2eyqA_



not modelled 97.4 13 PDB header:hydrolase
Chain: A: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor
99d1qdea_



not modelled 97.4 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
100d1c4oa1



not modelled 97.4 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
101c2gxqA_



not modelled 97.4 25 PDB header:hydrolase
Chain: A: PDB Molecule:heat resistant rna dependent atpase;
PDBTitle: hera n-terminal domain in complex with amp, crystal form 1
102c2zj2A_



not modelled 97.4 16 PDB header:hydrolase
Chain: A: PDB Molecule:putative ski2-type helicase;
PDBTitle: archaeal dna helicase hjm apo state in form 1
103d1sxje2



not modelled 97.4 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
104c1ojlF_



not modelled 97.4 18 PDB header:response regulator
Chain: F: PDB Molecule:transcriptional regulatory protein zrar;
PDBTitle: crystal structure of a sigma54-activator suggests the2 mechanism for the conformational switch necessary for3 sigma54 binding
105c2z4rB_



not modelled 97.4 15 PDB header:dna binding protein
Chain: B: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: crystal structure of domain iii from the thermotoga2 maritima replication initiation protein dnaa
106c3fe2B_



not modelled 97.4 20 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
107d1sxjd2



not modelled 97.4 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
108d1jbka_



not modelled 97.4 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
109d1q0ua_



not modelled 97.4 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
110c2c9oC_



not modelled 97.4 21 PDB header:hydrolase
Chain: C: PDB Molecule:ruvb-like 1;
PDBTitle: 3d structure of the human ruvb-like helicase ruvbl1
111c2z0mA_



not modelled 97.4 19 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
112d1a5ta2



not modelled 97.4 10 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
113d1sxjb2



not modelled 97.3 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
114c2v1xB_



not modelled 97.3 10 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent dna helicase q1;
PDBTitle: crystal structure of human recq-like dna helicase
115c1in8A_



not modelled 97.3 28 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
116c2f55C_



not modelled 97.3 21 PDB header:hydrolase/dna
Chain: C: PDB Molecule:polyprotein;
PDBTitle: two hepatitis c virus ns3 helicase domains complexed with2 the same strand of dna
117c3d8bB_



not modelled 97.3 17 PDB header:hydrolase
Chain: B: PDB Molecule:fidgetin-like protein 1;
PDBTitle: crystal structure of human fidgetin-like protein 1 in complex with adp
118c2v3cC_



not modelled 97.3 11 PDB header:signaling protein
Chain: C: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: crystal structure of the srp54-srp19-7s.s srp rna complex2 of m. jannaschii
119c3k1jA_



not modelled 97.3 14 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent protease lon;
PDBTitle: crystal structure of lon protease from thermococcus onnurineus na1
120d1s2ma1



not modelled 97.3 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain

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