Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP23331
DateThu Jan 5 11:39:23 GMT 2012
Unique Job ID5dc004b84284dc9c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2b8tA_
Top template information
PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from u.urealyticum in2 complex with thymidine
Confidence and coverage
Confidence:100.0% Coverage: 91%
187 residues ( 91% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MAQLYFYYSAMNAGKSTALLQSSYNYQERGMRTVVYTAEIDDRFGAGKVSSRIGLSSPAK
Secondary structure 
SS confidence 
Disorder  ??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LFNQNSSLFDEIRAEHEQQAIHCVLVDECQFLTRQQVYELSEVVDQLDIPVLCYGLRTDF
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  RGELFIGSQYLLAWSDKLVELKTICFCGRKASMVLRLDQAGRPYNEGEQVVIGGNERYVS
Secondary structure 
SS confidence 
Disorder 
?
?
?
Disorder confidence 
 
   .........190.........200.....
Sequence  VCRKHYKEALQVDSLTAIQERHRHD
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 2b8t chain A

3D model

Region: 1 - 189
Aligned: 187
Modelled: 189
Confidence: 100.0%
Identity: 26%
PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from u.urealyticum in2 complex with thymidine

Phyre2

PDB 3e2i chain A

3D model

Region: 2 - 187
Aligned: 169
Modelled: 186
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from s. aureus

Phyre2

PDB 1w4r chain C

3D model

Region: 2 - 188
Aligned: 158
Modelled: 166
Confidence: 100.0%
Identity: 28%
PDB header:transferase
Chain: C: PDB Molecule:thymidine kinase;
PDBTitle: structure of a type ii thymidine kinase with bound dttp

Phyre2

PDB 2orv chain B

3D model

Region: 2 - 188
Aligned: 158
Modelled: 166
Confidence: 100.0%
Identity: 28%
PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: human thymidine kinase 1 in complex with tp4a

Phyre2

PDB 2qq0 chain B

3D model

Region: 2 - 190
Aligned: 167
Modelled: 183
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from thermotoga maritima in complex with2 thymidine + appnhp

Phyre2

PDB 2ja1 chain A

3D model

Region: 1 - 187
Aligned: 181
Modelled: 187
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from b. cereus with ttp bound as phosphate2 donor.

Phyre2

PDB 1xx6 chain B

3D model

Region: 1 - 190
Aligned: 160
Modelled: 166
Confidence: 100.0%
Identity: 23%
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.

Phyre2

PDB 2b8t chain A domain 1

3D model

Region: 1 - 141
Aligned: 139
Modelled: 141
Confidence: 100.0%
Identity: 23%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Type II thymidine kinase

Phyre2

PDB 1xx6 chain A domain 1

3D model

Region: 1 - 142
Aligned: 129
Modelled: 135
Confidence: 100.0%
Identity: 22%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Type II thymidine kinase

Phyre2

PDB 1xbt chain A domain 1

3D model

Region: 2 - 142
Aligned: 118
Modelled: 120
Confidence: 100.0%
Identity: 23%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Type II thymidine kinase

Phyre2

PDB 2b8t chain A domain 2

3D model

Region: 142 - 187
Aligned: 46
Modelled: 46
Confidence: 99.5%
Identity: 37%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Type II thymidine kinase zinc finger

Phyre2

PDB 1xbt chain A domain 2

3D model

Region: 143 - 188
Aligned: 40
Modelled: 46
Confidence: 99.2%
Identity: 45%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Type II thymidine kinase zinc finger

Phyre2

PDB 2zro chain A

3D model

Region: 2 - 142
Aligned: 141
Modelled: 141
Confidence: 98.9%
Identity: 16%
PDB header:hydrolase
Chain: A: PDB Molecule:protein reca;
PDBTitle: msreca adp form iv

Phyre2

PDB 2j7p chain A

3D model

Region: 2 - 133
Aligned: 132
Modelled: 132
Confidence: 98.9%
Identity: 16%
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

Phyre2

PDB 1xx6 chain A domain 2

3D model

Region: 143 - 190
Aligned: 43
Modelled: 48
Confidence: 98.9%
Identity: 33%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Type II thymidine kinase zinc finger

Phyre2

PDB 3e1s chain A

3D model

Region: 1 - 142
Aligned: 130
Modelled: 131
Confidence: 98.9%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2

Phyre2

PDB 3b85 chain A

3D model

Region: 2 - 115
Aligned: 113
Modelled: 111
Confidence: 98.9%
Identity: 12%
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 3b9q chain A

3D model

Region: 2 - 105
Aligned: 104
Modelled: 104
Confidence: 98.9%
Identity: 13%
PDB header:protein transport
Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit
PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana

Phyre2

PDB 2j37 chain W

3D model

Region: 2 - 130
Aligned: 129
Modelled: 129
Confidence: 98.8%
Identity: 12%
PDB header:ribosome
Chain: W: PDB Molecule:signal recognition particle 54 kda protein
PDBTitle: model of mammalian srp bound to 80s rncs

Phyre2

PDB 2vbc chain A

3D model

Region: 2 - 114
Aligned: 113
Modelled: 113
Confidence: 98.8%
Identity: 12%
PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus

Phyre2
1
c2b8tA_
2
c3e2iA_
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c1w4rC_
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c2orvB_
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c2qq0B_
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c2ja1A_
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c1xx6B_
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d2b8ta1
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d1xx6a1
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d1xbta1
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d2b8ta2
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d1xbta2
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c2zroA_
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c2j7pA_
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d1xx6a2
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c3e1sA_
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c3b85A_
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c3b9qA_
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c2j37W_
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c2vbcA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2b8tA_
100.0 26 PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from u.urealyticum in2 complex with thymidine
2c3e2iA_
100.0 25 PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: crystal structure of thymidine kinase from s. aureus
3c1w4rC_
100.0 28 PDB header:transferase
Chain: C: PDB Molecule:thymidine kinase;
PDBTitle: structure of a type ii thymidine kinase with bound dttp
4c2orvB_
100.0 28 PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: human thymidine kinase 1 in complex with tp4a
5c2qq0B_
100.0 25 PDB header:transferase
Chain: B: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from thermotoga maritima in complex with2 thymidine + appnhp
6c2ja1A_
100.0 25 PDB header:transferase
Chain: A: PDB Molecule:thymidine kinase;
PDBTitle: thymidine kinase from b. cereus with ttp bound as phosphate2 donor.
7c1xx6B_
100.0 23 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.
8d2b8ta1
100.0 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Type II thymidine kinase
9d1xx6a1
100.0 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Type II thymidine kinase
10d1xbta1
100.0 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Type II thymidine kinase
11d2b8ta2
99.5 37 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:Type II thymidine kinase zinc finger
12d1xbta2
99.2 45 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:Type II thymidine kinase zinc finger
13c2zroA_
98.9 16 PDB header:hydrolase
Chain: A: PDB Molecule:protein reca;
PDBTitle: msreca adp form iv
14c2j7pA_
98.9 16 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
15d1xx6a2
98.9 33 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:Type II thymidine kinase zinc finger
16c3e1sA_
98.9 18 PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease v, subunit recd;
PDBTitle: structure of an n-terminal truncation of deinococcus radiodurans recd2
17c3b85A_
98.9 12 PDB header:hydrolase
Chain: A: PDB Molecule:phosphate starvation-inducible protein;
PDBTitle: crystal structure of predicted phosphate starvation-induced atpase2 phoh2 from corynebacterium glutamicum
18c3b9qA_
98.9 13 PDB header:protein transport
Chain: A: PDB Molecule:chloroplast srp receptor homolog, alpha subunit
PDBTitle: the crystal structure of cpftsy from arabidopsis thaliana
19c2j37W_
98.8 12 PDB header:ribosome
Chain: W: PDB Molecule:signal recognition particle 54 kda protein
PDBTitle: model of mammalian srp bound to 80s rncs
20c2vbcA_
98.8 12 PDB header:hydrolase
Chain: A: PDB Molecule:dengue 4 ns3 full-length protein;
PDBTitle: crystal structure of the ns3 protease-helicase from dengue2 virus
21c2cnwF_
not modelled 98.8 16 PDB header:signal recognition
Chain: F: PDB Molecule:cell division protein ftsy;
PDBTitle: gdpalf4 complex of the srp gtpases ffh and ftsy
22d1mo6a1
not modelled 98.8 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
23c3dm5A_
not modelled 98.8 11 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.
24c2iy3A_
not modelled 98.8 16 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
25c2recB_
not modelled 98.7 18 PDB header:helicase
PDB COMPND:
26d1u94a1
not modelled 98.7 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
27c3dmdA_
not modelled 98.7 11 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
28d1w36d1
not modelled 98.7 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
29c1xp8A_
not modelled 98.7 18 PDB header:dna binding protein
Chain: A: PDB Molecule:reca protein;
PDBTitle: "deinococcus radiodurans reca in complex with atp-gamma-s"
30d1ubea1
not modelled 98.7 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
31c3hr8A_
not modelled 98.7 16 PDB header:recombination
Chain: A: PDB Molecule:protein reca;
PDBTitle: crystal structure of thermotoga maritima reca
32c2og2A_
not modelled 98.7 12 PDB header:protein transport
Chain: A: PDB Molecule:putative signal recognition particle receptor;
PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana
33d1cr2a_
not modelled 98.7 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
34c2wv9A_
not modelled 98.7 13 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
35c2qy9A_
not modelled 98.6 12 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
36c2yhsA_
not modelled 98.6 12 PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsy;
PDBTitle: structure of the e. coli srp receptor ftsy
37d1xp8a1
not modelled 98.6 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
38c2v6jA_
not modelled 98.6 15 PDB header:hydrolase
Chain: A: PDB Molecule:rna helicase;
PDBTitle: kokobera virus helicase: mutant met47thr
39d1tf7a2
not modelled 98.6 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
40c1w36G_
not modelled 98.6 12 PDB header:recombination
Chain: G: PDB Molecule:exodeoxyribonuclease v alpha chain;
PDBTitle: recbcd:dna complex
41c1vmaA_
not modelled 98.6 13 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
42c1zu4A_
not modelled 98.6 16 PDB header:protein transport
Chain: A: PDB Molecule:ftsy;
PDBTitle: crystal structure of ftsy from mycoplasma mycoides- space2 group p21212
43c2jlrA_
not modelled 98.6 14 PDB header:hydrolase
Chain: A: PDB Molecule:serine protease subunit ns3;
PDBTitle: dengue virus 4 ns3 helicase in complex with amppnp
44c3bh0A_
not modelled 98.5 18 PDB header:replication
Chain: A: PDB Molecule:dnab-like replicative helicase;
PDBTitle: atpase domain of g40p
45d1yksa1
not modelled 98.5 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
46c2vyeA_
not modelled 98.5 17 PDB header:hydrolase
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: crystal structure of the dnac-ssdna complex
47c2v3cC_
not modelled 98.5 9 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
48c2j289_
not modelled 98.5 11 PDB header:ribosome
Chain: 9: PDB Molecule:signal recognition particle 54;
PDBTitle: model of e. coli srp bound to 70s rncs
49c2q6tB_
not modelled 98.4 14 PDB header:hydrolase
Chain: B: PDB Molecule:dnab replication fork helicase;
PDBTitle: crystal structure of the thermus aquaticus dnab monomer
50c3te6A_
not modelled 98.4 9 PDB header:gene regulation
Chain: A: PDB Molecule:regulatory protein sir3;
PDBTitle: crystal structure of the s. cerevisiae sir3 aaa+ domain
51c2ztsB_
not modelled 98.4 14 PDB header:atp-binding protein
Chain: B: PDB Molecule:putative uncharacterized protein ph0186;
PDBTitle: crystal structure of kaic-like protein ph0186 from2 hyperthermophilic archaea pyrococcus horikoshii ot3
52c2w0mA_
not modelled 98.4 15 PDB header:unknown function
Chain: A: PDB Molecule:sso2452;
PDBTitle: crystal structure of sso2452 from sulfolobus solfataricus2 p2
53d1qzxa3
not modelled 98.4 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
54c2z83A_
not modelled 98.4 12 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
55c2qeqA_
not modelled 98.4 17 PDB header:hydrolase
Chain: A: PDB Molecule:flavivirin protease ns3 catalytic subunit;
PDBTitle: crystal structure of kunjin virus ns3 helicase
56c3cmvG_
not modelled 98.4 17 PDB header:recombination
Chain: G: PDB Molecule:protein reca;
PDBTitle: mechanism of homologous recombination from the reca-2 ssdna/dsdna structures
57c1qzwC_
not modelled 98.4 12 PDB header:signaling protein/rna
Chain: C: PDB Molecule:signal recognition 54 kda protein;
PDBTitle: crystal structure of the complete core of archaeal srp and2 implications for inter-domain communication
58d1fnna2
not modelled 98.4 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
59c3bgwD_
not modelled 98.4 16 PDB header:replication
Chain: D: PDB Molecule:dnab-like replicative helicase;
PDBTitle: the structure of a dnab-like replicative helicase and its interactions2 with primase
60d1pjra1
not modelled 98.4 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
61d1g5ta_
not modelled 98.3 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
62c1ymfA_
not modelled 98.3 15 PDB header:hydrolase
Chain: A: PDB Molecule:genome polyprotein [contains: flavivirin
PDBTitle: crystal structure of yellow fever virus ns3 helicase2 complexed with adp
63d1g64b_
not modelled 98.3 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
64c1q57G_
not modelled 98.3 13 PDB header:transferase
Chain: G: PDB Molecule:dna primase/helicase;
PDBTitle: the crystal structure of the bifunctional primase-helicase of2 bacteriophage t7
65c2wjyA_
not modelled 98.3 16 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
66c1u9iA_
not modelled 98.3 14 PDB header:circadian clock protein
Chain: A: PDB Molecule:kaic;
PDBTitle: crystal structure of circadian clock protein kaic with phosphorylation2 sites
67d1tf7a1
not modelled 98.3 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
68c3pfiB_
not modelled 98.3 16 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
69c2kjqA_
not modelled 98.3 18 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.
70c2hcbC_
not modelled 98.2 17 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
71c2xzlA_
not modelled 98.2 19 PDB header:hydrolase/rna
Chain: A: PDB Molecule:atp-dependent helicase nam7;
PDBTitle: upf1-rna complex
72d1n0wa_
not modelled 98.2 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
73c1fnnB_
not modelled 98.2 13 PDB header:cell cycle
Chain: B: PDB Molecule:cell division control protein 6;
PDBTitle: crystal structure of cdc6p from pyrobaculum aerophilum
74d1uaaa1
not modelled 98.2 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
75d1a1va1
not modelled 98.2 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
76c2eyqA_
not modelled 98.2 12 PDB header:hydrolase
Chain: A: PDB Molecule:transcription-repair coupling factor;
PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor
77c3pvsA_
not modelled 98.2 11 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
78c3ec2A_
not modelled 98.2 10 PDB header:replication
Chain: A: PDB Molecule:dna replication protein dnac;
PDBTitle: crystal structure of the dnac helicase loader
79d1ls1a2
not modelled 98.2 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
80c2is6B_
not modelled 98.1 20 PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna helicase ii;
PDBTitle: crystal structure of uvrd-dna-adpmgf3 ternary complex
81c2dr3A_
not modelled 98.1 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0273 protein ph0284;
PDBTitle: crystal structure of reca superfamily atpase ph0284 from pyrococcus2 horikoshii ot3
82c2px0D_
not modelled 98.1 17 PDB header:biosynthetic protein
Chain: D: PDB Molecule:flagellar biosynthesis protein flhf;
PDBTitle: crystal structure of flhf complexed with gmppnp/mg(2+)
83d2eyqa3
not modelled 98.1 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
84c2ia5C_
not modelled 98.1 9 PDB header:transferase
Chain: C: PDB Molecule:polynucleotide kinase;
PDBTitle: t4 polynucleotide kinase/phosphatase with bound sulfate and2 magnesium.
85c3ldaA_
not modelled 98.1 18 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad51;
PDBTitle: yeast rad51 h352y filament interface mutant
86c3jvvA_
not modelled 98.1 12 PDB header:atp binding protein
Chain: A: PDB Molecule:twitching mobility protein;
PDBTitle: crystal structure of p. aeruginosa pilt with bound amp-pcp
87c2w58B_
not modelled 98.1 7 PDB header:hydrolase
Chain: B: PDB Molecule:primosome component (helicase loader);
PDBTitle: crystal structure of the dnai
88c1cu1B_
not modelled 98.1 15 PDB header:hydrolase
Chain: B: PDB Molecule:protein (protease/helicase ns3);
PDBTitle: crystal structure of an enzyme complex from hepatitis c2 virus
89d1p9ra_
not modelled 98.1 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
90d2bmfa2
not modelled 98.0 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RNA helicase
91c1szpC_
not modelled 98.0 16 PDB header:dna binding protein
Chain: C: PDB Molecule:dna repair protein rad51;
PDBTitle: a crystal structure of the rad51 filament
92c1ly1A_
not modelled 98.0 9 PDB header:transferase
Chain: A: PDB Molecule:polynucleotide kinase;
PDBTitle: structure and mechanism of t4 polynucleotide kinase
93d1ly1a_
not modelled 98.0 9 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
94c1sxjC_
not modelled 98.0 14 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)
95c2gk7A_
not modelled 98.0 17 PDB header:hydrolase
Chain: A: PDB Molecule:regulator of nonsense transcripts 1;
PDBTitle: structural and functional insights into the human upf1 helicase core
96c2yvuA_
not modelled 98.0 12 PDB header:transferase
Chain: A: PDB Molecule:probable adenylyl-sulfate kinase;
PDBTitle: crystal structure of ape1195
97d1ny5a2
not modelled 98.0 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
98c2pjrF_
not modelled 98.0 20 PDB header:hydrolase/dna
Chain: F: PDB Molecule:protein (helicase pcra);
PDBTitle: helicase product complex
99c3io5B_
not modelled 98.0 13 PDB header:dna binding protein
Chain: B: PDB Molecule:recombination and repair protein;
PDBTitle: crystal structure of a dimeric form of the uvsx recombinase core2 domain from enterobacteria phage t4
100d1szpa2
not modelled 98.0 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
101d1nlfa_
not modelled 98.0 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
102c2r2aB_
not modelled 98.0 14 PDB header:toxin
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of n-terminal domain of zonular occludens toxin from2 neisseria meningitidis
103c3kx2A_
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
104c2eyuA_
not modelled 98.0 11 PDB header:protein transport
Chain: A: PDB Molecule:twitching motility protein pilt;
PDBTitle: the crystal structure of the c-terminal domain of aquifex2 aeolicus pilt
105d2i1qa2
not modelled 97.9 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
106c1in8A_
not modelled 97.9 11 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
107c2qgzA_
not modelled 97.9 16 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
108c1sxjD_
not modelled 97.9 8 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)
109d1v5wa_
not modelled 97.9 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
110c3pxiB_
not modelled 97.9 15 PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc
111c3d8bB_
not modelled 97.9 18 PDB header:hydrolase
Chain: B: PDB Molecule:fidgetin-like protein 1;
PDBTitle: crystal structure of human fidgetin-like protein 1 in complex with adp
112d2qy9a2
not modelled 97.9 9 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
113c1sxjA_
not modelled 97.9 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)
114c3b9pA_
not modelled 97.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:cg5977-pa, isoform a;
PDBTitle: spastin
115c2v1uA_
not modelled 97.8 13 PDB header:replication
Chain: A: PDB Molecule:cell division control protein 6 homolog;
PDBTitle: structure of the aeropyrum pernix orc1 protein in complex2 with dna
116d1l8qa2
not modelled 97.8 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
117c1uaaB_
not modelled 97.8 18 PDB header:hydrolase/dna
Chain: B: PDB Molecule:protein (atp-dependent dna helicase rep.);
PDBTitle: e. coli rep helicase/dna complex
118d2gnoa2
not modelled 97.8 9 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
119c2gszE_
not modelled 97.8 12 PDB header:protein transport
Chain: E: PDB Molecule:twitching motility protein pilt;
PDBTitle: structure of a. aeolicus pilt with 6 monomers per2 asymmetric unit
120c1jr3E_
not modelled 97.8 9 PDB header:transferase
Chain: E: PDB Molecule:dna polymerase iii, delta' subunit;
PDBTitle: crystal structure of the processivity clamp loader gamma2 complex of e. coli dna polymerase iii

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