Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP71229
DateThu Jan 5 12:12:26 GMT 2012
Unique Job IDce53b58912a042eb

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1ny5A_
Top template information
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state
Confidence and coverage
Confidence:100.0% Coverage: 42%
279 residues ( 42% 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.
565 residues ( 84%) 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  MAMSDEAMFAPPQGITIEAVNGMLAERLAQKHGKASLLRAFIPLPPPFSPVQLIELHVLK
Secondary structure 





















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Disorder  ???????
??











































???


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











????????












??
???






????????





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   .........130.........140.........150.........160.........170.........180
Sequence  NWLARIITPVLQSWLNDEEQQVALRLLEKDRDHHRVLVDITNAVLSHLDLDDLIADVARE
Secondary structure 







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Disorder 

















?

??



???














?
??










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   .........190.........200.........210.........220.........230.........240
Sequence  IHHFFGLASVSMVLGDHRKNEKFSLWCSDLSASHCACLPRCMPGESVLLTQTLQTRQPTL
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Disorder 


























??????????????
??















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




??????
?????????????






















??









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





































???????????










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   .........370.........380.........390.........400.........410.........420
Sequence  VDIVAKSDSTVLICGETGTGKEVIARAIHQLSPRRDKPLVKINCAAIPASLLESELFGHD
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Disorder 




























?
?????























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   .........430.........440.........450.........460.........470.........480
Sequence  KGAFTGAINTHRGRFEIADGGTLFLDEIGDLPLELQPKLLRVLQEREIERLGGSRTIPVN
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Disorder 






????






































?
?






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   .........490.........500.........510.........520.........530.........540
Sequence  VRVIAATNRDLWQMVEDRQFRSDLFYRLNVFPLELPPLRDRPEDIPLLAKHFTQKMARHM
Secondary structure 

















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Disorder 















???







































?
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   .........550.........560.........570.........580.........590.........600
Sequence  NRAIDAIPTEALRQLMSWDWPGNVRELENVIERAVLLTRGNSLNLHLNVRQSRLLPTLNE
Secondary structure 






























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Disorder 

??
??



































??

?????????????
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   .........610.........620.........630.........640.........650.........660
Sequence  DSALRSSMAQLLHPTTPENDEEERQRIVQVLRETNGIVAGPRGAATRLGMKRTTLLSRMQ
Secondary structure 























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Disorder  ?????????????????

















?????



















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   .........670
Sequence  RLGISVREVL
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 1ny5 chain A

3D model

Region: 305 - 592
Aligned: 279
Modelled: 288
Confidence: 100.0%
Identity: 45%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state

Phyre2

PDB 3dzd chain A

3D model

Region: 346 - 584
Aligned: 238
Modelled: 239
Confidence: 100.0%
Identity: 47%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4 in the inactive2 state

Phyre2

PDB 2c99 chain A

3D model

Region: 347 - 589
Aligned: 236
Modelled: 243
Confidence: 100.0%
Identity: 45%
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

Phyre2

PDB 1ny5 chain A domain 2

3D model

Region: 346 - 589
Aligned: 244
Modelled: 244
Confidence: 100.0%
Identity: 49%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1ojl chain F

3D model

Region: 346 - 593
Aligned: 245
Modelled: 248
Confidence: 100.0%
Identity: 53%
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

Phyre2

PDB 3co5 chain B

3D model

Region: 350 - 518
Aligned: 132
Modelled: 146
Confidence: 100.0%
Identity: 26%
PDB header:transcription regulator
Chain: B: PDB Molecule:putative two-component system transcriptional response
PDBTitle: crystal structure of sigma-54 interaction domain of putative2 transcriptional response regulator from neisseria gonorrhoeae

Phyre2

PDB 3p01 chain C

3D model

Region: 141 - 317
Aligned: 168
Modelled: 177
Confidence: 99.9%
Identity: 15%
PDB header:signaling protein
Chain: C: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120

Phyre2

PDB 2vea chain A domain 1

3D model

Region: 157 - 320
Aligned: 164
Modelled: 164
Confidence: 99.9%
Identity: 13%
Fold: Profilin-like
Superfamily: GAF domain-like
Family: GAF domain

Phyre2

PDB 2o9c chain A domain 1

3D model

Region: 155 - 316
Aligned: 162
Modelled: 162
Confidence: 99.9%
Identity: 12%
Fold: Profilin-like
Superfamily: GAF domain-like
Family: GAF domain

Phyre2

PDB 3k2n chain B

3D model

Region: 151 - 322
Aligned: 172
Modelled: 172
Confidence: 99.9%
Identity: 22%
PDB header:transcription regulator
Chain: B: PDB Molecule:sigma-54-dependent transcriptional regulator;
PDBTitle: the crystal structure of sigma-54-dependent transcriptional2 regulator domain from chlorobium tepidum tls

Phyre2

PDB 1mc0 chain A

3D model

Region: 92 - 324
Aligned: 222
Modelled: 233
Confidence: 99.9%
Identity: 14%
PDB header:hydrolase
Chain: A: PDB Molecule:3',5'-cyclic nucleotide phosphodiesterase 2a;
PDBTitle: regulatory segment of mouse 3',5'-cyclic nucleotide phosphodiesterase2 2a, containing the gaf a and gaf b domains

Phyre2

PDB 3p01 chain A

3D model

Region: 137 - 316
Aligned: 171
Modelled: 180
Confidence: 99.9%
Identity: 15%
PDB header:signaling protein
Chain: A: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120

Phyre2

PDB 3trc chain A

3D model

Region: 150 - 320
Aligned: 166
Modelled: 167
Confidence: 99.9%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of the gaf domain from a phosphoenolpyruvate-protein2 phosphotransferase (ptsp) from coxiella burnetii

Phyre2

PDB 3ci6 chain B

3D model

Region: 152 - 321
Aligned: 163
Modelled: 169
Confidence: 99.9%
Identity: 17%
PDB header:transferase
Chain: B: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: crystal structure of the gaf domain from acinetobacter2 phosphoenolpyruvate-protein phosphotransferase

Phyre2

PDB 3oov chain A

3D model

Region: 159 - 320
Aligned: 162
Modelled: 162
Confidence: 99.9%
Identity: 12%
PDB header:signaling protein
Chain: A: PDB Molecule:methyl-accepting chemotaxis protein, putative;
PDBTitle: crystal structure of a methyl-accepting chemotaxis protein, residues2 122 to 287

Phyre2

PDB 2ool chain A domain 1

3D model

Region: 148 - 318
Aligned: 171
Modelled: 171
Confidence: 99.9%
Identity: 11%
Fold: Profilin-like
Superfamily: GAF domain-like
Family: GAF domain

Phyre2

PDB 3mmh chain A

3D model

Region: 148 - 315
Aligned: 155
Modelled: 168
Confidence: 99.9%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase;
PDBTitle: x-ray structure of free methionine-r-sulfoxide reductase from2 neisseria meningitidis in complex with its substrate

Phyre2

PDB 2zmf chain A

3D model

Region: 150 - 321
Aligned: 170
Modelled: 172
Confidence: 99.9%
Identity: 14%
PDB header:hydrolase
Chain: A: PDB Molecule:camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase
PDBTitle: crystal structure of the c-terminal gaf domain of human2 phosphodiesterase 10a

Phyre2

PDB 3pfi chain B

3D model

Region: 343 - 662
Aligned: 252
Modelled: 284
Confidence: 99.9%
Identity: 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

Phyre2

PDB 1ykd chain B

3D model

Region: 108 - 321
Aligned: 204
Modelled: 214
Confidence: 99.9%
Identity: 19%
PDB header:lyase
Chain: B: PDB Molecule:adenylate cyclase;
PDBTitle: crystal structure of the tandem gaf domains from a cyanobacterial2 adenylyl cyclase: novel modes of ligand-binding and dimerization

Phyre2

PDB 1ntc chain A

3D model

Region: 559 - 665
Aligned: 90
Modelled: 90
Confidence: 99.5%
Identity: 26%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: FIS-like

Phyre2
1

c1ny5A_
2

c3dzdA_
3

c2c99A_
4

d1ny5a2
5

c1ojlF_
6

c3co5B_
7

c3p01C_
8

d2veaa1
9

d2o9ca1
10

c3k2nB_
11

c1mc0A_
12

c3p01A_
13

c3trcA_
14

c3ci6B_
15

c3oovA_
16

d2oola1
17

c3mmhA_
18

c2zmfA_
19

c3pfiB_
20

c1ykdB_
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d1ntca_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1ny5A_



100.0 45 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state
2c3dzdA_



100.0 47 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4 in the inactive2 state
3c2c99A_



100.0 45 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
4d1ny5a2



100.0 49 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
5c1ojlF_



100.0 53 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
6c3co5B_



100.0 26 PDB header:transcription regulator
Chain: B: PDB Molecule:putative two-component system transcriptional response
PDBTitle: crystal structure of sigma-54 interaction domain of putative2 transcriptional response regulator from neisseria gonorrhoeae
7c3p01C_



99.9 15 PDB header:signaling protein
Chain: C: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120
8d2veaa1



99.9 13 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
9d2o9ca1



99.9 12 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
10c3k2nB_



99.9 22 PDB header:transcription regulator
Chain: B: PDB Molecule:sigma-54-dependent transcriptional regulator;
PDBTitle: the crystal structure of sigma-54-dependent transcriptional2 regulator domain from chlorobium tepidum tls
11c1mc0A_



99.9 14 PDB header:hydrolase
Chain: A: PDB Molecule:3',5'-cyclic nucleotide phosphodiesterase 2a;
PDBTitle: regulatory segment of mouse 3',5'-cyclic nucleotide phosphodiesterase2 2a, containing the gaf a and gaf b domains
12c3p01A_



99.9 15 PDB header:signaling protein
Chain: A: PDB Molecule:two-component response regulator;
PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120
13c3trcA_



99.9 17 PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of the gaf domain from a phosphoenolpyruvate-protein2 phosphotransferase (ptsp) from coxiella burnetii
14c3ci6B_



99.9 17 PDB header:transferase
Chain: B: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: crystal structure of the gaf domain from acinetobacter2 phosphoenolpyruvate-protein phosphotransferase
15c3oovA_



99.9 12 PDB header:signaling protein
Chain: A: PDB Molecule:methyl-accepting chemotaxis protein, putative;
PDBTitle: crystal structure of a methyl-accepting chemotaxis protein, residues2 122 to 287
16d2oola1



99.9 11 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
17c3mmhA_



99.9 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:methionine-r-sulfoxide reductase;
PDBTitle: x-ray structure of free methionine-r-sulfoxide reductase from2 neisseria meningitidis in complex with its substrate
18c2zmfA_



99.9 14 PDB header:hydrolase
Chain: A: PDB Molecule:camp and camp-inhibited cgmp 3',5'-cyclic phosphodiesterase
PDBTitle: crystal structure of the c-terminal gaf domain of human2 phosphodiesterase 10a
19c3pfiB_



99.9 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
20c1ykdB_



99.9 19 PDB header:lyase
Chain: B: PDB Molecule:adenylate cyclase;
PDBTitle: crystal structure of the tandem gaf domains from a cyanobacterial2 adenylyl cyclase: novel modes of ligand-binding and dimerization
21c3mf0A_



not modelled 99.9 12 PDB header:hydrolase
Chain: A: PDB Molecule:cgmp-specific 3',5'-cyclic phosphodiesterase;
PDBTitle: crystal structure of pde5a gaf domain (89-518)
22c3ibjB_



not modelled 99.9 17 PDB header:hydrolase
Chain: B: PDB Molecule:cgmp-dependent 3',5'-cyclic phosphodiesterase;
PDBTitle: x-ray structure of pde2a
23d1r6bx3



not modelled 99.8 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
24c3eeaB_



not modelled 99.8 16 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:gaf domain/hd domain protein;
PDBTitle: the crystal structure of the gaf domain/hd domain protein2 from geobacter sulfurreducens
25c1vhmB_



not modelled 99.8 12 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:protein yebr;
PDBTitle: crystal structure of an hypothetical protein
26d1vhma_



not modelled 99.8 12 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
27c1qvrB_



not modelled 99.8 20 PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb
28c2lb5A_



not modelled 99.8 20 PDB header:transferase
Chain: A: PDB Molecule:sensor histidine kinase;
PDBTitle: refined structural basis for the photoconversion of a phytochrome to2 the activated far-red light-absorbing form
29c2vjwA_



not modelled 99.8 18 PDB header:hydrolase
Chain: A: PDB Molecule:gaf family protein;
PDBTitle: crystal structure of the second gaf domain of devs from2 mycobacterium smegmatis
30c1in8A_



not modelled 99.8 19 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
31c3pxiB_



not modelled 99.8 18 PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc
32c3e0yA_



not modelled 99.8 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved domain protein;
PDBTitle: the crystal structure of a conserved domain from a protein of2 geobacter sulfurreducens pca
33d1mc0a1



not modelled 99.8 15 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
34c3nbxX_



not modelled 99.8 19 PDB header:hydrolase
Chain: X: PDB Molecule:atpase rava;
PDBTitle: crystal structure of e. coli rava (regulatory atpase variant a) in2 complex with adp
35c3o5yA_



not modelled 99.8 20 PDB header:transcription regulator
Chain: A: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of the gaf domain of a two-component sensor2 histidine kinase from bacillus halodurans to 2.45a
36c3dbaB_



not modelled 99.8 10 PDB header:hydrolase
Chain: B: PDB Molecule:cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit
PDBTitle: crystal structure of the cgmp-bound gaf a domain from the2 photoreceptor phosphodiesterase 6c
37c1r6bX_



not modelled 99.8 20 PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa
38c3ksiA_



not modelled 99.8 10 PDB header:oxidoreductase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: structure of frmsr of staphylococcus aureus (complex with 2-propanol)
39c2qybA_



not modelled 99.8 18 PDB header:membrane protein
Chain: A: PDB Molecule:membrane protein, putative;
PDBTitle: crystal structure of the gaf domain region of putative membrane2 protein from geobacter sulfurreducens pca
40d1um8a_



not modelled 99.8 25 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
41d1qvra3



not modelled 99.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
42d2k2na1



not modelled 99.8 20 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
43c2w3gA_



not modelled 99.8 15 PDB header:transferase
Chain: A: PDB Molecule:two component sensor histidine kinase devs (gaf
PDBTitle: air-oxidized structure of the first gaf domain of2 mycobacterium tuberculosis doss
44c3hcyB_



not modelled 99.8 13 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative two-component sensor histidine kinase protein;
PDBTitle: the crystal structure of the domain of putative two-component sensor2 histidine kinase protein from sinorhizobium meliloti 1021
45d3c2wa1



not modelled 99.8 15 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
46d1l8qa2



not modelled 99.7 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
47c3c2wB_



not modelled 99.7 14 PDB header:signaling protein
Chain: B: PDB Molecule:bacteriophytochrome;
PDBTitle: crystal structure of the photosensory core domain of p.2 aeruginosa bacteriophytochrome pabphp in the pfr state
48c3pvsA_



not modelled 99.7 19 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
49c2oolA_



not modelled 99.7 12 PDB header:signaling protein
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the chromophore-binding domain of an unusual2 bacteriophytochrome rpbphp3 from r. palustris
50c3k1jA_



not modelled 99.7 24 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent protease lon;
PDBTitle: crystal structure of lon protease from thermococcus onnurineus na1
51c2veaA_



not modelled 99.7 12 PDB header:transferase
Chain: A: PDB Molecule:phytochrome-like protein cph1;
PDBTitle: the complete sensory module of the cyanobacterial2 phytochrome cph1 in the pr-state.
52d1mc0a2



not modelled 99.7 14 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
53c2o9bA_



not modelled 99.6 12 PDB header:transferase
Chain: A: PDB Molecule:bacteriophytochrome;
PDBTitle: crystal structure of bacteriophytochrome chromophore binding domain
54c2hcbC_



not modelled 99.6 19 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
55c2z4rB_



not modelled 99.6 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
56c3bosA_



not modelled 99.6 14 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
57c2k31A_



not modelled 99.6 13 PDB header:hydrolase
Chain: A: PDB Molecule:phosphodiesterase 5a, cgmp-specific;
PDBTitle: solution structure of cgmp-binding gaf domain of2 phosphodiesterase 5
58d1g8pa_



not modelled 99.6 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
59c1nsfA_



not modelled 99.6 19 PDB header:protein transport
Chain: A: PDB Molecule:n-ethylmaleimide sensitive factor;
PDBTitle: d2 hexamerization domain of n-ethylmaleimide sensitive factor (nsf)
60c3hteC_



not modelled 99.6 20 PDB header:motor protein
Chain: C: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: crystal structure of nucleotide-free hexameric clpx
61c3e98B_



not modelled 99.6 14 PDB header:unknown function
Chain: B: PDB Molecule:gaf domain of unknown function;
PDBTitle: crystal structure of a gaf domain containing protein that belongs to2 pfam duf484 family (pa5279) from pseudomonas aeruginosa at 2.43 a3 resolution
62d1f5ma_



not modelled 99.6 13 Fold:Profilin-like
Superfamily:GAF domain-like
Family:GAF domain
63c1hqcB_



not modelled 99.6 15 PDB header:hydrolase
Chain: B: PDB Molecule:ruvb;
PDBTitle: structure of ruvb from thermus thermophilus hb8
64c2xssB_



not modelled 99.5 12 PDB header:hydrolase
Chain: B: PDB Molecule:cgmp-specific 3', 5'-cyclic phosphodiesterase;
PDBTitle: crystal structure of gafb from the human phosphodiesterase 5
65c3f8tA_



not modelled 99.5 19 PDB header:hydrolase
Chain: A: PDB Molecule:predicted atpase involved in replication control,
PDBTitle: crystal structure analysis of a full-length mcm homolog2 from methanopyrus kandleri
66c2r44A_



not modelled 99.5 12 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
67d1ntca_



99.5 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
68d1g41a_



not modelled 99.5 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
69d1fnna2



not modelled 99.5 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
70d1ofha_



not modelled 99.5 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
71d1in4a2



not modelled 99.4 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
72d1ixsb2



not modelled 99.4 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
73c2c9oC_



not modelled 99.4 22 PDB header:hydrolase
Chain: C: PDB Molecule:ruvb-like 1;
PDBTitle: 3d structure of the human ruvb-like helicase ruvbl1
74d1sxjd2



not modelled 99.4 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
75d1etob_



not modelled 99.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
76d1d2na_



not modelled 99.3 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
77d1fipa_



not modelled 99.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
78c2dhrC_



not modelled 99.3 22 PDB header:hydrolase
Chain: C: PDB Molecule:ftsh;
PDBTitle: whole cytosolic region of atp-dependent metalloprotease2 ftsh (g399l)
79c3f9vA_



not modelled 99.3 19 PDB header:hydrolase
Chain: A: PDB Molecule:minichromosome maintenance protein mcm;
PDBTitle: crystal structure of a near full-length archaeal mcm: functional2 insights for an aaa+ hexameric helicase
80c3e7lD_



not modelled 99.3 22 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
81d1etxa_



not modelled 99.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
82c2chgB_



not modelled 99.3 20 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
83d1njfa_



not modelled 99.2 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
84c2ce7B_



not modelled 99.2 21 PDB header:cell division protein
Chain: B: PDB Molecule:cell division protein ftsh;
PDBTitle: edta treated
85c3eihB_



not modelled 99.2 21 PDB header:protein transport
Chain: B: PDB Molecule:vacuolar protein sorting-associated protein 4;
PDBTitle: crystal structure of s.cerevisiae vps4 in the presence of atpgammas
86c3b9pA_



not modelled 99.2 21 PDB header:hydrolase
Chain: A: PDB Molecule:cg5977-pa, isoform a;
PDBTitle: spastin
87d1iqpa2



not modelled 99.2 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
88c1xwiA_



not modelled 99.2 20 PDB header:protein transport
Chain: A: PDB Molecule:skd1 protein;
PDBTitle: crystal structure of vps4b
89d1umqa_



not modelled 99.1 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
90c1umqA_



not modelled 99.1 16 PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
91d1g2ha_



not modelled 99.1 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
92d1qvra2



not modelled 99.1 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
93c2p65A_



not modelled 99.1 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pf08_0063;
PDBTitle: crystal structure of the first nucleotide binding domain of2 chaperone clpb1, putative, (pv089580) from plasmodium vivax
94c2kjqA_



not modelled 99.1 21 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.
95d1sxjc2



not modelled 99.1 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
96c2r65A_



not modelled 99.1 22 PDB header:hydrolase
Chain: A: PDB Molecule:cell division protease ftsh homolog;
PDBTitle: crystal structure of helicobacter pylori atp dependent protease, ftsh2 adp complex
97d2ce7a2



not modelled 99.1 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
98d1sxjb2



not modelled 99.1 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
99c1xxhB_



not modelled 99.1 21 PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii subunit gamma;
PDBTitle: atpgs bound e. coli clamp loader complex
100c3h4mC_



not modelled 99.1 18 PDB header:hydrolase
Chain: C: PDB Molecule:proteasome-activating nucleotidase;
PDBTitle: aaa atpase domain of the proteasome- activating nucleotidase
101c1sxjD_



not modelled 99.0 14 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)
102d1w5sa2



not modelled 99.0 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
103c3u5zM_



not modelled 99.0 18 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
104c1fnnB_



not modelled 99.0 13 PDB header:cell cycle
Chain: B: PDB Molecule:cell division control protein 6;
PDBTitle: crystal structure of cdc6p from pyrobaculum aerophilum
105c1sxjC_



not modelled 99.0 17 PDB header:replication
Chain: C: PDB Molecule:activator 1 40 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
106c2zamA_



not modelled 99.0 19 PDB header:protein transport
Chain: A: PDB Molecule:vacuolar protein sorting-associating protein 4b;
PDBTitle: crystal structure of mouse skd1/vps4b apo-form
107d1r6bx2



not modelled 99.0 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
108c3d8bB_



not modelled 98.9 21 PDB header:hydrolase
Chain: B: PDB Molecule:fidgetin-like protein 1;
PDBTitle: crystal structure of human fidgetin-like protein 1 in complex with adp
109c1sxjB_



not modelled 98.9 15 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)
110d1lv7a_



not modelled 98.9 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
111c3hu2C_



not modelled 98.9 33 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
112c1iy2A_



not modelled 98.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent metalloprotease ftsh;
PDBTitle: crystal structure of the ftsh atpase domain from thermus2 thermophilus
113c2qbyB_



not modelled 98.9 20 PDB header:replication/dna
Chain: B: PDB Molecule:cell division control protein 6 homolog 3;
PDBTitle: crystal structure of a heterodimer of cdc6/orc1 initiators2 bound to origin dna (from s. solfataricus)
114d1jbka_



not modelled 98.9 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
115c2chvE_



not modelled 98.9 20 PDB header:dna-binding protein
Chain: E: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c adpnp complex
116c2qz4A_



not modelled 98.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:paraplegin;
PDBTitle: human paraplegin, aaa domain in complex with adp
117c3cf1C_



not modelled 98.9 23 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
118d1e32a2



not modelled 98.9 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
119c2v1uA_



not modelled 98.8 17 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
120c1iqpF_



not modelled 98.8 20 PDB header:replication
Chain: F: PDB Molecule:rfcs;
PDBTitle: crystal structure of the clamp loader small subunit from2 pyrococcus furiosus

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