Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP39393
DateThu Jan 5 12:00:28 GMT 2012
Unique Job ID59cfd90441049a96

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2v1xB_
Top template information
PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent dna helicase q1;
PDBTitle: crystal structure of human recq-like dna helicase
Confidence and coverage
Confidence: 99.5% Coverage: 9%
83 residues ( 9% of your sequence) have been modelled with 99.5% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MYVNQRQNCDCGSPVYEVAFCNDCNEPHLLARDKKGKLVQWENKGGDEFSLQDEVPVEHD
Secondary structure 
SS confidence 
Disorder  ??????????
???
?
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ATEEKVEKENSFQPPLIIAAGETSEAGYTLQRLDRQTRRIGVINNDSIPLIINDIEQVCS
Secondary structure 
SS confidence 
Disorder  ???
????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  ASGCGYRGMSGKQPFRRALLGGPFYVTNIVPTVLEYCQDFTSDEGKEGVGPDSLPGRGRR
Secondary structure 
SS confidence 
Disorder 
?????????
?
??
?????
?
?????????????
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LITFTDSRQGTARMAVRMQQEAERSRLRGSVVEILSWHQRTQTSTAPNANADLEKLAARA
Secondary structure 
SS confidence 
Disorder 
?
?????????????
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  KQAREQAEEYRSWGMPDQAKLSQAQAEQLEQAYQAATGGKAATILVSRTWTEMVNELKER
Secondary structure 
SS confidence 
Disorder 
?????
??
??
???
????????????
??
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  ADIRGPVLQYNHYLKPEVFNENGGPLKLSEMLLFREFMRRPKRTNSLETQGLVQVGYQGL
Secondary structure 
SS confidence 
Disorder  ?????
?
??
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  EKIHKSPLHWQEKGLTLDDWRDFLKVTLDHYVRESNFTQLDDELKNWIGSRFSSKFVRNP
Secondary structure 
SS confidence 
Disorder 
??
??
???????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  ESKDPEDNQNRRWPQIRNGNVSHRLAKLLMLGAGFKTVNAATIDIINTWLKEAWAQLTGP
Secondary structure 
SS confidence 
Disorder  ??????????
??????
???????
??
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  LAVLKPDGNRFYLPKEHMTFSLITDAWICPVTNKILDTAFKGLTPYLPTHISFEHLTLAQ
Secondary structure 
SS confidence 
Disorder  ?
??
??
?
?
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  YDTFVAQKVTMPEIWKLDRSQEDYAEGLAKARDWVSHDPLIAQLRSENVWTDINDRVVEG
Secondary structure 
SS confidence 
Disorder 
?
?????
??
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  GFYYRTAEHSAQQSSERLQSYEKMFKNGQLNVLNCSTTMEMGVDTDRVMTLASRSQQATI
Secondary structure 
SS confidence 
Disorder  ???
?????
??
?
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  PGPEWHLNDELVVRSLGYKTVELNEFILPAKATNAVERVKDIQIHKQLNGPLSQFGQRFW
Secondary structure 
SS confidence 
Disorder  ????????????
??
??
??
???????????????????
??
??????
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  DVLFNDHEEAQSLMNNTRITGVHYTDRYLQNPVALALLGSILRPLKTKLTDGAEVTLDTL
Secondary structure 
SS confidence 
Disorder 
???
??
????
?????
?
Disorder confidence 
 
   .........790.........800.........810.........820.........830.........840
Sequence  FKDKDRPGNRPFHDWMSIADFQDFADQWFAAALGRPVELTVFDSPRDIPHHRKLTVTFED
Secondary structure 
SS confidence 
Disorder  ???????
???????
Disorder confidence 
 
   .........850.........860.........870.........880.........890.........900
Sequence  GQVLKIRFDQGMGYWRINFSSQWHYFDFRDDVSFQLVKMAQACKEGNVANSEESWATDVL
Secondary structure 
SS confidence 
Disorder 
??
???????????
Disorder confidence 
 
   ......
Sequence  VEVIAS
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 2v1x chain B

3D model

Region: 603 - 711
Aligned: 83
Modelled: 87
Confidence: 99.5%
Identity: 12%
PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent dna helicase q1;
PDBTitle: crystal structure of human recq-like dna helicase

Phyre2

PDB 2p6r chain A domain 4

3D model

Region: 606 - 714
Aligned: 84
Modelled: 87
Confidence: 99.4%
Identity: 15%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1oyw chain A

3D model

Region: 603 - 711
Aligned: 83
Modelled: 87
Confidence: 99.4%
Identity: 10%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase;
PDBTitle: structure of the recq catalytic core

Phyre2

PDB 1oyw chain A domain 3

3D model

Region: 603 - 711
Aligned: 83
Modelled: 87
Confidence: 99.3%
Identity: 10%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 3rc8 chain A

3D model

Region: 603 - 750
Aligned: 112
Modelled: 126
Confidence: 99.3%
Identity: 15%
PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase supv3l1, mitochondrial;
PDBTitle: human mitochondrial helicase suv3 in complex with short rna fragment

Phyre2

PDB 2db3 chain D

3D model

Region: 602 - 711
Aligned: 84
Modelled: 88
Confidence: 99.3%
Identity: 13%
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

Phyre2

PDB 2xgj chain A

3D model

Region: 609 - 711
Aligned: 78
Modelled: 81
Confidence: 99.3%
Identity: 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

Phyre2

PDB 4a4z chain A

3D model

Region: 609 - 709
Aligned: 76
Modelled: 79
Confidence: 99.2%
Identity: 21%
PDB header:hydrolase
Chain: A: PDB Molecule:antiviral helicase ski2;
PDBTitle: crystal structure of the s. cerevisiae dexh helicase ski2 bound to2 amppnp

Phyre2

PDB 2i4i chain A

3D model

Region: 602 - 714
Aligned: 85
Modelled: 91
Confidence: 99.2%
Identity: 11%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx3x;
PDBTitle: crystal structure of human dead-box rna helicase ddx3x

Phyre2

PDB 1gm5 chain A

3D model

Region: 604 - 728
Aligned: 99
Modelled: 103
Confidence: 99.2%
Identity: 13%
PDB header:helicase
Chain: A: PDB Molecule:recg;
PDBTitle: structure of recg bound to three-way dna junction

Phyre2

PDB 3l9o chain A

3D model

Region: 609 - 711
Aligned: 75
Modelled: 81
Confidence: 99.2%
Identity: 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

Phyre2

PDB 2eyq chain A domain 5

3D model

Region: 592 - 715
Aligned: 98
Modelled: 102
Confidence: 99.2%
Identity: 19%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1hv8 chain B

3D model

Region: 602 - 713
Aligned: 86
Modelled: 90
Confidence: 99.2%
Identity: 14%
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

Phyre2

PDB 3fht chain A

3D model

Region: 602 - 711
Aligned: 84
Modelled: 88
Confidence: 99.1%
Identity: 17%
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

Phyre2

PDB 3i32 chain A

3D model

Region: 602 - 713
Aligned: 81
Modelled: 90
Confidence: 99.1%
Identity: 15%
PDB header:rna binding protein,hydrolase
Chain: A: PDB Molecule:heat resistant rna dependent atpase;
PDBTitle: dimeric structure of a hera helicase fragment including the c-terminal2 reca domain, the dimerization domain, and the rna binding domain

Phyre2

PDB 1s2m chain A

3D model

Region: 603 - 715
Aligned: 87
Modelled: 91
Confidence: 99.1%
Identity: 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

Phyre2

PDB 2hxy chain C

3D model

Region: 603 - 713
Aligned: 85
Modelled: 89
Confidence: 99.1%
Identity: 13%
PDB header:hydrolase
Chain: C: PDB Molecule:probable atp-dependent rna helicase ddx48;
PDBTitle: crystal structure of human apo-eif4aiii

Phyre2

PDB 1gm5 chain A domain 4

3D model

Region: 602 - 714
Aligned: 87
Modelled: 91
Confidence: 99.0%
Identity: 15%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Tandem AAA-ATPase domain

Phyre2

PDB 1xtk chain A

3D model

Region: 606 - 711
Aligned: 80
Modelled: 84
Confidence: 99.0%
Identity: 14%
PDB header:gene regulation
Chain: A: PDB Molecule:probable atp-dependent rna helicase p47;
PDBTitle: structure of decd to dead mutation of human uap56

Phyre2

PDB 2zj2 chain A

3D model

Region: 609 - 699
Aligned: 66
Modelled: 66
Confidence: 99.0%
Identity: 12%
PDB header:hydrolase
Chain: A: PDB Molecule:putative ski2-type helicase;
PDBTitle: archaeal dna helicase hjm apo state in form 1

Phyre2

PDB 1yuz chain B

3D model

Region: 495 - 532
Aligned: 38
Modelled: 38
Confidence: 82.8%
Identity: 11%
PDB header:oxidoreductase
Chain: B: PDB Molecule:nigerythrin;
PDBTitle: partially reduced state of nigerythrin

Phyre2

PDB 2hr5 chain B

3D model

Region: 495 - 532
Aligned: 38
Modelled: 38
Confidence: 82.4%
Identity: 16%
PDB header:metal binding protein
Chain: B: PDB Molecule:rubrerythrin;
PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form

Phyre2

PDB 3ndj chain A

3D model

Region: 8 - 29
Aligned: 22
Modelled: 22
Confidence: 80.2%
Identity: 36%
PDB header:transferase
Chain: A: PDB Molecule:methyltransferase;
PDBTitle: x-ray structure of a c-3'-methyltransferase in complex with s-2 adenosyl-l-homocysteine and sugar product

Phyre2

PDB 1dvb chain A

3D model

Region: 468 - 540
Aligned: 57
Modelled: 57
Confidence: 79.5%
Identity: 14%
PDB header:electron transport
Chain: A: PDB Molecule:rubrerythrin;
PDBTitle: rubrerythrin

Phyre2

PDB 3k7a chain M

3D model

Region: 3 - 27
Aligned: 25
Modelled: 25
Confidence: 71.8%
Identity: 20%
PDB header:transcription
Chain: M: PDB Molecule:transcription initiation factor iib;
PDBTitle: crystal structure of an rna polymerase ii-tfiib complex

Phyre2

PDB 3cng chain C

3D model

Region: 7 - 39
Aligned: 33
Modelled: 33
Confidence: 68.3%
Identity: 24%
PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea

Phyre2
1
c2v1xB_
2
d2p6ra4
3
c1oywA_
4
d1oywa3
5
c3rc8A_
6
c2db3D_
7
c2xgjA_
8
c4a4zA_
9
c2i4iA_
10
c1gm5A_
11
c3l9oA_
12
d2eyqa5
13
c1hv8B_
14
c3fhtA_
15
c3i32A_
16
c1s2mA_
17
c2hxyC_
18
d1gm5a4
19
c1xtkA_
20
c2zj2A_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
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73
74
75
76
77
78
79
80
81
82
83
84
85
c1yuzB_
86
87
c2hr5B_
88
c3ndjA_
89
c1dvbA_
90
91
c3k7aM_
92
93
94
c3cngC_
95
96
97
98
99
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101
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103
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154



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2v1xB_
99.5 12 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent dna helicase q1;
PDBTitle: crystal structure of human recq-like dna helicase
2d2p6ra4
99.4 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
3c1oywA_
99.4 10 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase;
PDBTitle: structure of the recq catalytic core
4d1oywa3
99.3 10 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
5c3rc8A_
99.3 15 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase supv3l1, mitochondrial;
PDBTitle: human mitochondrial helicase suv3 in complex with short rna fragment
6c2db3D_
99.3 13 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
7c2xgjA_
99.3 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
8c4a4zA_
99.2 21 PDB header:hydrolase
Chain: A: PDB Molecule:antiviral helicase ski2;
PDBTitle: crystal structure of the s. cerevisiae dexh helicase ski2 bound to2 amppnp
9c2i4iA_
99.2 11 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx3x;
PDBTitle: crystal structure of human dead-box rna helicase ddx3x
10c1gm5A_
99.2 13 PDB header:helicase
Chain: A: PDB Molecule:recg;
PDBTitle: structure of recg bound to three-way dna junction
11c3l9oA_
99.2 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
12d2eyqa5
99.2 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
13c1hv8B_
99.2 14 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
14c3fhtA_
99.1 17 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
15c3i32A_
99.1 15 PDB header:rna binding protein,hydrolase
Chain: A: PDB Molecule:heat resistant rna dependent atpase;
PDBTitle: dimeric structure of a hera helicase fragment including the c-terminal2 reca domain, the dimerization domain, and the rna binding domain
16c1s2mA_
99.1 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
17c2hxyC_
99.1 13 PDB header:hydrolase
Chain: C: PDB Molecule:probable atp-dependent rna helicase ddx48;
PDBTitle: crystal structure of human apo-eif4aiii
18d1gm5a4
99.0 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
19c1xtkA_
99.0 14 PDB header:gene regulation
Chain: A: PDB Molecule:probable atp-dependent rna helicase p47;
PDBTitle: structure of decd to dead mutation of human uap56
20c2zj2A_
99.0 12 PDB header:hydrolase
Chain: A: PDB Molecule:putative ski2-type helicase;
PDBTitle: archaeal dna helicase hjm apo state in form 1
21c2va8A_
not modelled 99.0 17 PDB header:hydrolase
Chain: A: PDB Molecule:ski2-type helicase;
PDBTitle: dna repair helicase hel308
22c2fwrA_
not modelled 99.0 14 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad25;
PDBTitle: structure of archaeoglobus fulgidis xpb
23c1wp9D_
not modelled 99.0 16 PDB header:hydrolase
Chain: D: PDB Molecule:atp-dependent rna helicase, putative;
PDBTitle: crystal structure of pyrococcus furiosus hef helicase domain
24c2z0mA_
not modelled 99.0 8 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
25c3earA_
not modelled 99.0 11 PDB header:hydrolase
Chain: A: PDB Molecule:hera;
PDBTitle: novel dimerization motif in the dead box rna helicase hera: form 1,2 partial dimer
26d1s2ma2
not modelled 99.0 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
27d1t5la2
not modelled 99.0 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
28c2vsxA_
not modelled 99.0 13 PDB header:translation/hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase eif4a;
PDBTitle: crystal structure of a translation initiation complex
29c3tmiA_
not modelled 99.0 11 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent rna helicase ddx58;
PDBTitle: structural basis for rna recognition and activation of rig-i
30c1c4oA_
not modelled 98.9 10 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
31c3i5yA_
not modelled 98.9 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
32d2j0sa2
not modelled 98.9 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
33c2fzlA_
not modelled 98.9 13 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad25, xpb;
PDBTitle: structure of c-terminal domain of archaeoglobus fulgidus xpb
34d1t5ia_
not modelled 98.9 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
35c2eyqA_
not modelled 98.9 18 PDB header:hydrolase
Chain: A: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor
36c3ewsA_
not modelled 98.8 20 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx19b;
PDBTitle: human dead-box rna-helicase ddx19 in complex with adp
37c2d7dA_
not modelled 98.8 10 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
38d1c4oa2
not modelled 98.8 10 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
39d1hv8a2
not modelled 98.8 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
40d1wp9a2
not modelled 98.7 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
41c2hjvB_
not modelled 98.7 12 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase dbpa;
PDBTitle: structure of the second domain (residues 207-368) of the2 bacillus subtilis yxin protein
42c3pexA_
not modelled 98.7 11 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dbp5;
PDBTitle: s. cerevisiae dbp5 l327v bound to gle1 h337r and ip6
43d1fuka_
not modelled 98.7 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
44c2jlrA_
not modelled 98.7 13 PDB header:hydrolase
Chain: A: PDB Molecule:serine protease subunit ns3;
PDBTitle: dengue virus 4 ns3 helicase in complex with amppnp
45c2ocaA_
not modelled 98.7 13 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent dna helicase uvsw;
PDBTitle: the crystal structure of t4 uvsw
46c2v6jA_
not modelled 98.7 12 PDB header:hydrolase
Chain: A: PDB Molecule:rna helicase;
PDBTitle: kokobera virus helicase: mutant met47thr
47c2p6nA_
not modelled 98.6 12 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase ddx41;
PDBTitle: human dead-box rna helicase ddx41, helicase domain
48d1jr6a_
not modelled 98.6 7 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
49c2p6uA_
not modelled 98.6 12 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
50d2fwra1
not modelled 98.6 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
51d2g2ja1
not modelled 98.6 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
52c3oiyB_
not modelled 98.6 10 PDB header:isomerase
Chain: B: PDB Molecule:reverse gyrase helicase domain;
PDBTitle: helicase domain of reverse gyrase from thermotoga maritima
53c2vbcA_
not modelled 98.5 13 PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus
54d1tf5a4
not modelled 98.5 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
55c3tbkA_
not modelled 98.5 11 PDB header:hydrolase
Chain: A: PDB Molecule:rig-i helicase domain;
PDBTitle: mouse rig-i atpase domain
56c3kx2A_
not modelled 98.5 11 PDB header:hydrolase
Chain: A: PDB Molecule:pre-mrna-splicing factor atp-dependent rna
PDBTitle: crystal structure of prp43p in complex with adp
57c3bxzA_
not modelled 98.4 11 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
58c2jgnB_
not modelled 98.4 11 PDB header:hydrolase
Chain: B: PDB Molecule:atp-dependent rna helicase ddx3x;
PDBTitle: ddx3 helicase domain
59c2kbfA_
not modelled 98.4 11 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dbp5;
PDBTitle: solution structure of carboxyl-terminal domain of dbp5p
60c2wv9A_
not modelled 98.3 12 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
61d1a1va2
not modelled 98.3 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
62c2z83A_
not modelled 98.2 9 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
63c1gl9B_
not modelled 98.2 19 PDB header:topoisomerase
Chain: B: PDB Molecule:reverse gyrase;
PDBTitle: archaeoglobus fulgidus reverse gyrase complexed with adpnp
64d1gkub2
not modelled 98.0 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Helicase-like "domain" of reverse gyrase
65c1ymfA_
not modelled 98.0 5 PDB header:hydrolase
Chain: A: PDB Molecule:genome polyprotein [contains: flavivirin
PDBTitle: crystal structure of yellow fever virus ns3 helicase2 complexed with adp
66d2bmfa2
not modelled 97.9 6 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
67c1a1vA_
not modelled 97.8 11 PDB header:hydrolase/dna
Chain: A: PDB Molecule:protein (ns3 protein);
PDBTitle: hepatitis c virus ns3 helicase domain complexed with single2 stranded sdna
68c2qeqA_
not modelled 97.7 4 PDB header:hydrolase
Chain: A: PDB Molecule:flavivirin protease ns3 catalytic subunit;
PDBTitle: crystal structure of kunjin virus ns3 helicase
69c3h1tA_
not modelled 97.7 14 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
70c2w74B_
not modelled 97.5 13 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
71c2f55C_
not modelled 96.9 5 PDB header:hydrolase/dna
Chain: C: PDB Molecule:polyprotein;
PDBTitle: two hepatitis c virus ns3 helicase domains complexed with2 the same strand of dna
72d8ohma2
not modelled 96.8 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
73c1z63A_
not modelled 96.7 9 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
74c3mwyW_
not modelled 96.7 15 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
75c1z3iX_
not modelled 96.5 8 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
76d1nkta4
not modelled 96.3 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
77c3dmqA_
not modelled 96.0 14 PDB header:hydrolase
Chain: A: PDB Molecule:rna polymerase-associated protein rapa;
PDBTitle: crystal structure of rapa, a swi2/snf2 protein that2 recycles rna polymerase during transcription
78c3crw1_
not modelled 95.0 12 PDB header:hydrolase
Chain: 1: PDB Molecule:xpd/rad3 related dna helicase;
PDBTitle: "xpd_apo"
79c3dl8B_
not modelled 94.6 15 PDB header:protein transport
Chain: B: PDB Molecule:protein translocase subunit seca;
PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca
80c2fsgA_
not modelled 93.9 13 PDB header:protein transport
Chain: A: PDB Molecule:preprotein translocase seca subunit;
PDBTitle: complex seca:atp from escherichia coli
81c1tf2A_
not modelled 93.5 16 PDB header:protein transport
Chain: A: PDB Molecule:preprotein translocase seca subunit;
PDBTitle: crystal structure of seca:adp in an open conformation from2 bacillus subtilis
82d1z3ix1
not modelled 88.4 8 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
83d1yksa2
not modelled 88.0 8 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
84c1cu1B_
not modelled 84.1 12 PDB header:hydrolase
Chain: B: PDB Molecule:protein (protease/helicase ns3);
PDBTitle: crystal structure of an enzyme complex from hepatitis c2 virus
85c1yuzB_
82.8 11 PDB header:oxidoreductase
Chain: B: PDB Molecule:nigerythrin;
PDBTitle: partially reduced state of nigerythrin
86d1z5za1
not modelled 82.7 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
87c2hr5B_
82.4 16 PDB header:metal binding protein
Chain: B: PDB Molecule:rubrerythrin;
PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form
88c3ndjA_
80.2 36 PDB header:transferase
Chain: A: PDB Molecule:methyltransferase;
PDBTitle: x-ray structure of a c-3'-methyltransferase in complex with s-2 adenosyl-l-homocysteine and sugar product
89c1dvbA_
79.5 14 PDB header:electron transport
Chain: A: PDB Molecule:rubrerythrin;
PDBTitle: rubrerythrin
90c1z5zB_
not modelled 78.0 13 PDB header:hydrolase/recombination
Chain: B: PDB Molecule:helicase of the snf2/rad54 family;
PDBTitle: sulfolobus solfataricus swi2/snf2 atpase c-terminal domain
91c3k7aM_
71.8 20 PDB header:transcription
Chain: M: PDB Molecule:transcription initiation factor iib;
PDBTitle: crystal structure of an rna polymerase ii-tfiib complex
92d1dl6a_
not modelled 71.8 19 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
93d1wffa_
not modelled 70.9 22 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
94c3cngC_
68.3 24 PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea
95c2w00B_
not modelled 61.8 14 PDB header:hydrolase
Chain: B: PDB Molecule:hsdr;
PDBTitle: crystal structure of the hsdr subunit of the ecor124i2 restriction enzyme in complex with atp
96c2gb5B_
not modelled 61.0 35 PDB header:hydrolase
Chain: B: PDB Molecule:nadh pyrophosphatase;
PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution
97d1wfla_
not modelled 60.1 22 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
98d1yuza2
not modelled 58.7 13 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
99c3h0gL_
not modelled 55.0 47 PDB header:transcription
Chain: L: PDB Molecule:dna-directed rna polymerases i, ii, and iii
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
100d1nnqa2
not modelled 54.6 16 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
101d1wg2a_
not modelled 54.0 21 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
102d1pfta_
not modelled 53.1 28 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
103c2ja6L_
not modelled 52.6 35 PDB header:transferase
Chain: L: PDB Molecule:dna-directed rna polymerases i, ii, and iii 7.7
PDBTitle: cpd lesion containing rna polymerase ii elongation complex2 b
104c1m98A_
not modelled 51.4 20 PDB header:unknown function
Chain: A: PDB Molecule:orange carotenoid protein;
PDBTitle: crystal structure of orange carotenoid protein
105d1wfha_
not modelled 51.3 21 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
106d2j0151
not modelled 50.6 20 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
107c3bvoA_
not modelled 48.3 37 PDB header:chaperone
Chain: A: PDB Molecule:co-chaperone protein hscb, mitochondrial precursor;
PDBTitle: crystal structure of human co-chaperone protein hscb
108c3eswA_
not modelled 48.2 47 PDB header:hydrolase
Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine
PDBTitle: complex of yeast pngase with glcnac2-iac.
109c1i3qI_
not modelled 48.1 40 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd
PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution
110d1wfpa_
not modelled 47.1 21 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
111c2pziA_
not modelled 46.1 35 PDB header:transferase
Chain: A: PDB Molecule:probable serine/threonine-protein kinase pkng;
PDBTitle: crystal structure of protein kinase pkng from mycobacterium2 tuberculosis in complex with tetrahydrobenzothiophene ax20017
112d2zjrz1
not modelled 45.4 20 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
113c3pfqA_
not modelled 44.5 47 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c beta type;
PDBTitle: crystal structure and allosteric activation of protein kinase c beta2 ii
114c2ysoA_
not modelled 40.8 38 PDB header:transcription
Chain: A: PDB Molecule:zinc finger protein 95 homolog;
PDBTitle: solution structure of the c2h2 type zinc finger (region 656-2 688) of human zinc finger protein 95 homolog
115c2ps3A_
not modelled 40.5 11 PDB header:metal transport
Chain: A: PDB Molecule:high-affinity zinc uptake system protein znua;
PDBTitle: structure and metal binding properties of znua, a2 periplasmic zinc transporter from escherichia coli
116c2kwqA_
not modelled 39.3 26 PDB header:dna binding protein
Chain: A: PDB Molecule:protein mcm10 homolog;
PDBTitle: mcm10 c-terminal dna binding domain
117c2js4A_
not modelled 38.5 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0434 protein bb2007;
PDBTitle: solution nmr structure of bordetella bronchiseptica protein2 bb2007. northeast structural genomics consortium target3 bor54
118d1lkoa2
not modelled 37.6 13 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
119d1jwhc_
not modelled 36.8 22 Fold:Rubredoxin-like
Superfamily:Casein kinase II beta subunit
Family:Casein kinase II beta subunit
120d2ayja1
not modelled 35.9 28 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L40e

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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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