Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP07604
DateThu Jan 5 11:00:21 GMT 2012
Unique Job ID75324cd7032b3115

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: 50%
255 residues ( 50% 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.
506 residues ( 99%) 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  MRLEVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPIGRIYLNFAELEFESFSSLMAEIRR
Secondary structure 















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Disorder  ??










































?
?











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   .........70.........80.........90.........100.........110.........120
Sequence  IAGVTDVRTVPWMPSEREHLALSALLEALPEPVLSVDMKSKVDMANPASCQLFGQKLDRL
Secondary structure 












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Disorder  ?

?







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




















??????






















??







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   .........190.........200.........210.........220.........230.........240
Sequence  MLRSTIRMGRQLQNVAAQDVSAFSQIVAVSPKMKHVVEQAQKLAMLSAPLLITGDTGTGK
Secondary structure 

















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Disorder 














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































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







???????






















???
?
















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





















?
























???








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























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Disorder 






























?

??
?





















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   .........430.........440.........450.........460.........470.........480
Sequence  NAIYRALTQLDGYELRPQDILLPDYDAATVAVGEDAMEGSLDEITSRFERSVLTQLYRNY
Secondary structure 























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Disorder 



















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



















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   .........490.........500.........510...
Sequence  PSTRKLAKRLGVSHTAIANKLREYGLSQKKNEE
Secondary structure 














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Disorder  ??




















??????????
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Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 1ny5 chain A

3D model

Region: 187 - 441
Aligned: 255
Modelled: 255
Confidence: 100.0%
Identity: 41%
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: 196 - 437
Aligned: 241
Modelled: 242
Confidence: 100.0%
Identity: 44%
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: 206 - 446
Aligned: 241
Modelled: 241
Confidence: 100.0%
Identity: 37%
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: 205 - 441
Aligned: 237
Modelled: 237
Confidence: 100.0%
Identity: 44%
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: 205 - 446
Aligned: 242
Modelled: 242
Confidence: 100.0%
Identity: 41%
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: 209 - 370
Aligned: 132
Modelled: 146
Confidence: 100.0%
Identity: 23%
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 2jhe chain B

3D model

Region: 1 - 190
Aligned: 189
Modelled: 190
Confidence: 100.0%
Identity: 95%
PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)

Phyre2

PDB 3pfi chain B

3D model

Region: 201 - 504
Aligned: 253
Modelled: 304
Confidence: 99.9%
Identity: 15%
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 1r6b chain X domain 3

3D model

Region: 204 - 430
Aligned: 223
Modelled: 227
Confidence: 99.9%
Identity: 20%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3pxi chain B

3D model

Region: 203 - 428
Aligned: 212
Modelled: 225
Confidence: 99.8%
Identity: 18%
PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc

Phyre2

PDB 1qvr chain B

3D model

Region: 203 - 428
Aligned: 217
Modelled: 226
Confidence: 99.8%
Identity: 19%
PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb

Phyre2

PDB 1um8 chain A

3D model

Region: 213 - 428
Aligned: 209
Modelled: 216
Confidence: 99.8%
Identity: 17%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1r6b chain X

3D model

Region: 210 - 427
Aligned: 212
Modelled: 218
Confidence: 99.8%
Identity: 18%
PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa

Phyre2

PDB 3pvs chain A

3D model

Region: 202 - 490
Aligned: 251
Modelled: 289
Confidence: 99.8%
Identity: 14%
PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa

Phyre2

PDB 1in8 chain A

3D model

Region: 202 - 504
Aligned: 253
Modelled: 296
Confidence: 99.8%
Identity: 15%
PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v

Phyre2

PDB 1qvr chain A domain 3

3D model

Region: 203 - 428
Aligned: 217
Modelled: 226
Confidence: 99.8%
Identity: 19%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3nbx chain X

3D model

Region: 214 - 434
Aligned: 206
Modelled: 216
Confidence: 99.8%
Identity: 21%
PDB header:hydrolase
Chain: X: PDB Molecule:atpase rava;
PDBTitle: crystal structure of e. coli rava (regulatory atpase variant a) in2 complex with adp

Phyre2

PDB 1l8q chain A domain 2

3D model

Region: 198 - 428
Aligned: 204
Modelled: 231
Confidence: 99.8%
Identity: 18%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3k1j chain A

3D model

Region: 215 - 440
Aligned: 221
Modelled: 226
Confidence: 99.7%
Identity: 23%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent protease lon;
PDBTitle: crystal structure of lon protease from thermococcus onnurineus na1

Phyre2

PDB 2hcb chain C

3D model

Region: 198 - 430
Aligned: 204
Modelled: 233
Confidence: 99.7%
Identity: 20%
PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus

Phyre2

PDB 1ntc chain A

3D model

Region: 411 - 507
Aligned: 85
Modelled: 85
Confidence: 99.5%
Identity: 24%
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

c2jheB_
8

c3pfiB_
9

d1r6bx3
10

c3pxiB_
11

c1qvrB_
12

d1um8a_
13

c1r6bX_
14

c3pvsA_
15

c1in8A_
16

d1qvra3
17

c3nbxX_
18

d1l8qa2
19

c3k1jA_
20

c2hcbC_
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d1ntca_
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Detailed template information 

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



100.0 41 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 44 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 37 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 44 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
5c1ojlF_



100.0 41 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 23 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
7c2jheB_



100.0 95 PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)
8c3pfiB_



99.9 15 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
9d1r6bx3



99.9 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
10c3pxiB_



99.8 18 PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc
11c1qvrB_



99.8 19 PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb
12d1um8a_



99.8 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
13c1r6bX_



99.8 18 PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa
14c3pvsA_



99.8 14 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
15c1in8A_



99.8 15 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
16d1qvra3



99.8 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
17c3nbxX_



99.8 21 PDB header:hydrolase
Chain: X: PDB Molecule:atpase rava;
PDBTitle: crystal structure of e. coli rava (regulatory atpase variant a) in2 complex with adp
18d1l8qa2



99.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
19c3k1jA_



99.7 23 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent protease lon;
PDBTitle: crystal structure of lon protease from thermococcus onnurineus na1
20c2hcbC_



99.7 20 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
21c3bosA_



not modelled 99.7 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
22c1nsfA_



not modelled 99.6 18 PDB header:protein transport
Chain: A: PDB Molecule:n-ethylmaleimide sensitive factor;
PDBTitle: d2 hexamerization domain of n-ethylmaleimide sensitive factor (nsf)
23c2z4rB_



not modelled 99.6 16 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
24c3f8tA_



not modelled 99.6 16 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
25c3hteC_



not modelled 99.6 16 PDB header:motor protein
Chain: C: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: crystal structure of nucleotide-free hexameric clpx
26c2r44A_



not modelled 99.6 14 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
27c1hqcB_



not modelled 99.6 13 PDB header:hydrolase
Chain: B: PDB Molecule:ruvb;
PDBTitle: structure of ruvb from thermus thermophilus hb8
28c2c9oC_



not modelled 99.5 18 PDB header:hydrolase
Chain: C: PDB Molecule:ruvb-like 1;
PDBTitle: 3d structure of the human ruvb-like helicase ruvbl1
29d1g41a_



not modelled 99.5 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
30c2wkqA_



not modelled 99.5 12 PDB header:transferase, cell adhesion
Chain: A: PDB Molecule:nph1-1, ras-related c3 botulinum toxin substrate
PDBTitle: structure of a photoactivatable rac1 containing the lov22 c450a mutant
31d1g8pa_



not modelled 99.5 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
32d1ntca_



99.5 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
33d1ixsb2



not modelled 99.5 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
34d1in4a2



not modelled 99.5 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
35d1ofha_



not modelled 99.5 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
36c3f9vA_



not modelled 99.5 18 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
37d1fnna2



not modelled 99.5 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
38d1d2na_



not modelled 99.4 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
39d1etob_



not modelled 99.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
40c3mfxA_



not modelled 99.4 11 PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef family protein;
PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b
41c3e7lD_



not modelled 99.3 15 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain
42d1g2ha_



not modelled 99.3 54 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
43c2dhrC_



not modelled 99.3 18 PDB header:hydrolase
Chain: C: PDB Molecule:ftsh;
PDBTitle: whole cytosolic region of atp-dependent metalloprotease2 ftsh (g399l)
44d1iqpa2



not modelled 99.3 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
45c2chgB_



not modelled 99.3 19 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
46d1fipa_



not modelled 99.3 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
47d1sxjd2



not modelled 99.3 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
48c3mxqC_



not modelled 99.3 11 PDB header:transferase
Chain: C: PDB Molecule:sensor protein;
PDBTitle: crystal structure of sensory box sensor histidine kinase from vibrio2 cholerae
49c3b33A_



not modelled 99.3 22 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus
50c3eihB_



not modelled 99.3 15 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
51c3oloB_



not modelled 99.3 14 PDB header:transferase
Chain: B: PDB Molecule:two-component sensor histidine kinase;
PDBTitle: crystal structure of a pas domain from two-component sensor histidine2 kinase
52d1etxa_



not modelled 99.3 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
53c3caxA_



not modelled 99.3 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pf0695;
PDBTitle: crystal structure of uncharacterized protein pf0695
54d1njfa_



not modelled 99.2 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
55c1xwiA_



not modelled 99.2 16 PDB header:protein transport
Chain: A: PDB Molecule:skd1 protein;
PDBTitle: crystal structure of vps4b
56c3b9pA_



not modelled 99.2 19 PDB header:hydrolase
Chain: A: PDB Molecule:cg5977-pa, isoform a;
PDBTitle: spastin
57c2kjqA_



not modelled 99.2 20 PDB header:replication
Chain: A: PDB Molecule:dnaa-related protein;
PDBTitle: solution structure of protein nmb1076 from neisseria meningitidis.2 northeast structural genomics consortium target mr101b.
58c2gj3A_



not modelled 99.2 17 PDB header:transferase
Chain: A: PDB Molecule:nitrogen fixation regulatory protein;
PDBTitle: crystal structure of the fad-containing pas domain of the2 protein nifl from azotobacter vinelandii.
59d1nwza_



not modelled 99.2 10 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
60c3hu2C_



not modelled 99.2 19 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
61c1v9yA_



not modelled 99.2 14 PDB header:signaling protein
Chain: A: PDB Molecule:heme pas sensor protein;
PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form)
62d1v9ya_



not modelled 99.2 14 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
63c3lyxA_



not modelled 99.2 16 PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef domain protein;
PDBTitle: crystal structure of the pas domain of the protein cps_12912 from colwellia psychrerythraea. northeast structural3 genomics consortium target id csr222b
64c2ce7B_



not modelled 99.2 19 PDB header:cell division protein
Chain: B: PDB Molecule:cell division protein ftsh;
PDBTitle: edta treated
65c3mqoB_



not modelled 99.2 13 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: the crystal structure of the pas domain in complex with isopropanol of2 a transcriptional regulator in the luxr family from burkholderia3 thailandensis to 1.7a
66d2ce7a2



not modelled 99.2 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
67c2v1bA_



not modelled 99.2 11 PDB header:transferase
Chain: A: PDB Molecule:nph1-1;
PDBTitle: n- and c-terminal helices of oat lov2 (404-546) are2 involved in light-induced signal transduction (room3 temperature (293k) light structure of lov2 (404-546))
68c3luqC_



not modelled 99.2 8 PDB header:transferase
Chain: C: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of a pas domain from a sensory box2 histidine kinase regulator from geobacter sulfurreducens to3 2.5a
69c2r78D_



not modelled 99.1 21 PDB header:transferase
Chain: D: PDB Molecule:sensor protein;
PDBTitle: crystal structure of a domain of the sensory box sensor2 histidine kinase/response regulator from geobacter3 sulfurreducens
70c3bwlA_



not modelled 99.1 14 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of pas domain of htr-like protein from haloarcula2 marismortui
71c3h4mC_



not modelled 99.1 15 PDB header:hydrolase
Chain: C: PDB Molecule:proteasome-activating nucleotidase;
PDBTitle: aaa atpase domain of the proteasome- activating nucleotidase
72c3mjqB_



not modelled 99.1 11 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the pas domain of q24qt8_deshy protein from2 desulfitobacterium hafniense. northeast structural genomics3 consortium target dhr85c.
73c2r65A_



not modelled 99.1 24 PDB header:hydrolase
Chain: A: PDB Molecule:cell division protease ftsh homolog;
PDBTitle: crystal structure of helicobacter pylori atp dependent protease, ftsh2 adp complex
74c3fg8B_



not modelled 99.1 11 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein rha05790;
PDBTitle: crystal structure of pas domain of rha05790
75c2w0nA_



not modelled 99.1 18 PDB header:transferase
Chain: A: PDB Molecule:sensor protein dcus;
PDBTitle: plasticity of pas domain and potential role for signal2 transduction in the histidine-kinase dcus
76c3cf1C_



not modelled 99.1 18 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
77d1ew0a_



not modelled 99.1 12 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
78d1sxjb2



not modelled 99.1 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
79c1umqA_



not modelled 99.1 14 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
80d1umqa_



not modelled 99.1 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
81d1sxjc2



not modelled 99.1 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
82d1w5sa2



not modelled 99.1 11 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
83d1qvra2



not modelled 99.1 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
84c3d8bB_



not modelled 99.0 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
85d1ixza_



not modelled 99.0 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
86c1iy2A_



not modelled 99.0 21 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent metalloprotease ftsh;
PDBTitle: crystal structure of the ftsh atpase domain from thermus2 thermophilus
87c2zamA_



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
88c3u5zM_



not modelled 99.0 14 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
89c2pr6A_



not modelled 99.0 14 PDB header:flavoprotein, signaling protein
Chain: A: PDB Molecule:blue-light photoreceptor;
PDBTitle: structural basis for light-dependent signaling in the dimeric lov2 photosensor ytva (light structure)
90c3a0vA_



not modelled 99.0 13 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m)
91c1fnnB_



not modelled 99.0 10 PDB header:cell cycle
Chain: B: PDB Molecule:cell division control protein 6;
PDBTitle: crystal structure of cdc6p from pyrobaculum aerophilum
92c2p65A_



not modelled 99.0 16 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
93d1otda_



not modelled 99.0 10 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
94d1mzua_



not modelled 99.0 13 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
95d1lv7a_



not modelled 99.0 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
96c3a0rA_



not modelled 99.0 12 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of histidine kinase thka (tm1359) in complex with2 response regulator protein trra (tm1360)
97d1y28a_



not modelled 99.0 12 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
98c1xxhB_



not modelled 99.0 20 PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii subunit gamma;
PDBTitle: atpgs bound e. coli clamp loader complex
99d1r6bx2



not modelled 98.9 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
100c2chvE_



not modelled 98.9 17 PDB header:dna-binding protein
Chain: E: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c adpnp complex
101c1sxjC_



not modelled 98.9 16 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)
102c2v1uA_



not modelled 98.9 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
103c2x8aA_



not modelled 98.9 14 PDB header:nuclear protein
Chain: A: PDB Molecule:nuclear valosin-containing protein-like;
PDBTitle: human nuclear valosin containing protein like (nvl), c-2 terminal aaa-atpase domain
104c2qbyA_



not modelled 98.9 13 PDB header:replication/dna
Chain: A: PDB Molecule:cell division control protein 6 homolog 1;
PDBTitle: crystal structure of a heterodimer of cdc6/orc1 initiators2 bound to origin dna (from s. solfataricus)
105c1sxjA_



not modelled 98.9 19 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)
106c3k3dA_



not modelled 98.9 9 PDB header:signaling protein
Chain: A: PDB Molecule:protein rv1364c/mt1410;
PDBTitle: the n-terminal pas domain crystal structure of rv1364c from2 mycobacterium tuberculosis at 2.3 angstrom
107c1sxjB_



not modelled 98.9 17 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)
108c3fc7B_



not modelled 98.9 14 PDB header:transferase
Chain: B: PDB Molecule:htr-like protein;
PDBTitle: the crystal structure of a domain of htr-like protein from haloarcula2 marismortui atcc 43049
109d1xj3a1



not modelled 98.9 13 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
110c2l4rA_



not modelled 98.9 12 PDB header:transport protein
Chain: A: PDB Molecule:potassium voltage-gated channel subfamily h member 2;
PDBTitle: nmr solution structure of the n-terminal pas domain of herg
111c2qkpD_



not modelled 98.9 9 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of c-terminal domain of smu_1151c from streptococcus2 mutans
112c3kx0X_



not modelled 98.9 15 PDB header:signaling protein
Chain: X: PDB Molecule:uncharacterized protein rv1364c/mt1410;
PDBTitle: crystal structure of the pas domain of rv1364c
113c2qbyB_



not modelled 98.9 19 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)
114c2qz4A_



not modelled 98.9 17 PDB header:hydrolase
Chain: A: PDB Molecule:paraplegin;
PDBTitle: human paraplegin, aaa domain in complex with adp
115c2vlgD_



not modelled 98.9 3 PDB header:transferase
Chain: D: PDB Molecule:sporulation kinase a;
PDBTitle: kina pas-a domain, homodimer
116d1n9la_



not modelled 98.9 13 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
117d1sxja2



not modelled 98.9 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
118c1sxjD_



not modelled 98.8 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)
119d1bywa_



not modelled 98.8 12 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
120c1s3sA_



not modelled 98.8 18 PDB header:protein binding
Chain: A: PDB Molecule:transitional endoplasmic reticulum atpase (ter
PDBTitle: crystal structure of aaa atpase p97/vcp nd1 in complex with2 p47 c

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