Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A6H1
DateThu Jan 5 11:03:08 GMT 2012
Unique Job ID05d5740f05df52fa

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1e94e_
Top template information
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
Confidence and coverage
Confidence:100.0% Coverage: 82%
346 residues ( 82% 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  MTDKRKDGSGKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEIKEVAPHRE
Secondary structure 
























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Disorder  ???????????












?

???
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?????????
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   .........70.........80.........90.........100.........110.........120
Sequence  RSALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGP
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Disorder  ??????






























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







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   .........130.........140.........150.........160.........170.........180
Sequence  TGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGI
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   .........190.........200.........210.........220.........230.........240
Sequence  VYIDEIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFLQVDT
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Disorder 







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











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




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







?????






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






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?


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   .........310.........320.........330.........340.........350.........360
Sequence  IPEFIGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAK
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   .........370.........380.........390.........400.........410.........420
Sequence  KAMARKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSKPLLIYGKPEAQQ
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Disorder 




?


















???

???

















?????????
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   ....
Sequence  ASGE
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 1e94 chain E

3D model

Region: 62 - 411
Aligned: 346
Modelled: 350
Confidence: 100.0%
Identity: 28%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1um8 chain A

3D model

Region: 62 - 412
Aligned: 309
Modelled: 328
Confidence: 100.0%
Identity: 57%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1qvr chain B

3D model

Region: 42 - 399
Aligned: 295
Modelled: 306
Confidence: 100.0%
Identity: 23%
PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb

Phyre2

PDB 1g41 chain A

3D model

Region: 66 - 413
Aligned: 288
Modelled: 307
Confidence: 100.0%
Identity: 41%
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: 41 - 408
Aligned: 297
Modelled: 316
Confidence: 100.0%
Identity: 23%
PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa

Phyre2

PDB 3pxi chain B

3D model

Region: 68 - 399
Aligned: 245
Modelled: 286
Confidence: 100.0%
Identity: 25%
PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc

Phyre2

PDB 1ofh chain A

3D model

Region: 66 - 414
Aligned: 293
Modelled: 308
Confidence: 100.0%
Identity: 40%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3hte chain C

3D model

Region: 64 - 413
Aligned: 283
Modelled: 311
Confidence: 100.0%
Identity: 93%
PDB header:motor protein
Chain: C: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: crystal structure of nucleotide-free hexameric clpx

Phyre2

PDB 1r6b chain X domain 3

3D model

Region: 55 - 399
Aligned: 274
Modelled: 286
Confidence: 100.0%
Identity: 23%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1qvr chain A domain 3

3D model

Region: 55 - 399
Aligned: 282
Modelled: 305
Confidence: 100.0%
Identity: 23%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3cf1 chain C

3D model

Region: 75 - 339
Aligned: 229
Modelled: 254
Confidence: 99.9%
Identity: 19%
PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx

Phyre2

PDB 1ny5 chain A

3D model

Region: 12 - 381
Aligned: 286
Modelled: 295
Confidence: 99.9%
Identity: 19%
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 2c99 chain A

3D model

Region: 78 - 393
Aligned: 233
Modelled: 256
Confidence: 99.9%
Identity: 21%
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 3dzd chain A

3D model

Region: 19 - 381
Aligned: 271
Modelled: 290
Confidence: 99.9%
Identity: 18%
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 2dhr chain C

3D model

Region: 76 - 386
Aligned: 222
Modelled: 245
Confidence: 99.9%
Identity: 24%
PDB header:hydrolase
Chain: C: PDB Molecule:ftsh;
PDBTitle: whole cytosolic region of atp-dependent metalloprotease2 ftsh (g399l)

Phyre2

PDB 1ny5 chain A domain 2

3D model

Region: 78 - 381
Aligned: 224
Modelled: 229
Confidence: 99.9%
Identity: 18%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 3pfi chain B

3D model

Region: 76 - 381
Aligned: 185
Modelled: 211
Confidence: 99.9%
Identity: 25%
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 3hu2 chain C

3D model

Region: 75 - 405
Aligned: 240
Modelled: 247
Confidence: 99.9%
Identity: 23%
PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs

Phyre2

PDB 1ojl chain F

3D model

Region: 77 - 381
Aligned: 225
Modelled: 243
Confidence: 99.9%
Identity: 22%
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 3eih chain B

3D model

Region: 76 - 387
Aligned: 222
Modelled: 242
Confidence: 99.9%
Identity: 23%
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

Phyre2

PDB 2ds8 chain A

3D model

Region: 10 - 51
Aligned: 42
Modelled: 42
Confidence: 98.9%
Identity: 100%
PDB header:metal binding protein, protein binding
Chain: A: PDB Molecule:atp-dependent clp protease atp-binding subunit
PDBTitle: structure of the zbd-xb complex

Phyre2

PDB 2ds5 chain A domain 1

3D model

Region: 13 - 49
Aligned: 37
Modelled: 37
Confidence: 98.7%
Identity: 100%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: ClpX chaperone zinc binding domain

Phyre2

PDB 1ovx chain B

3D model

Region: 13 - 49
Aligned: 37
Modelled: 37
Confidence: 98.7%
Identity: 100%
PDB header:metal binding protein
Chain: B: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: nmr structure of the e. coli clpx chaperone zinc binding domain dimer

Phyre2
1

d1e94e_
2

d1um8a_
3

c1qvrB_
4

d1g41a_
5

c1r6bX_
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c3pxiB_
7

d1ofha_
8

c3hteC_
9

d1r6bx3
10

d1qvra3
11

c3cf1C_
12

c1ny5A_
13

c2c99A_
14

c3dzdA_
15

c2dhrC_
16

d1ny5a2
17

c3pfiB_
18

c3hu2C_
19

c1ojlF_
20

c3eihB_
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c2ds8A_
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d2ds5a1
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c1ovxB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1e94e_



100.0 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
2d1um8a_



100.0 57 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
3c1qvrB_



100.0 23 PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb
4d1g41a_



100.0 41 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
5c1r6bX_



100.0 23 PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa
6c3pxiB_



100.0 25 PDB header:protein binding
Chain: B: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca108:clpc
7d1ofha_



100.0 40 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
8c3hteC_



100.0 93 PDB header:motor protein
Chain: C: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: crystal structure of nucleotide-free hexameric clpx
9d1r6bx3



100.0 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
10d1qvra3



100.0 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
11c3cf1C_



99.9 19 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
12c1ny5A_



99.9 19 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state
13c2c99A_



99.9 21 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
14c3dzdA_



99.9 18 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4 in the inactive2 state
15c2dhrC_



99.9 24 PDB header:hydrolase
Chain: C: PDB Molecule:ftsh;
PDBTitle: whole cytosolic region of atp-dependent metalloprotease2 ftsh (g399l)
16d1ny5a2



99.9 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
17c3pfiB_



99.9 25 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
18c3hu2C_



99.9 23 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
19c1ojlF_



99.9 22 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
20c3eihB_



99.9 23 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
21c3b9pA_



not modelled 99.8 26 PDB header:hydrolase
Chain: A: PDB Molecule:cg5977-pa, isoform a;
PDBTitle: spastin
22c2r44A_



not modelled 99.8 23 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
23c1xwiA_



not modelled 99.8 23 PDB header:protein transport
Chain: A: PDB Molecule:skd1 protein;
PDBTitle: crystal structure of vps4b
24c1s3sA_



not modelled 99.8 23 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
25c3pvsA_



not modelled 99.8 30 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
26c3m6aC_



not modelled 99.8 21 PDB header:hydrolase
Chain: C: PDB Molecule:atp-dependent protease la 1;
PDBTitle: crystal structure of bacillus subtilis lon c-terminal domain
27c3d8bB_



not modelled 99.8 24 PDB header:hydrolase
Chain: B: PDB Molecule:fidgetin-like protein 1;
PDBTitle: crystal structure of human fidgetin-like protein 1 in complex with adp
28d1g8pa_



not modelled 99.8 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
29c3h4mC_



not modelled 99.8 25 PDB header:hydrolase
Chain: C: PDB Molecule:proteasome-activating nucleotidase;
PDBTitle: aaa atpase domain of the proteasome- activating nucleotidase
30c2zamA_



not modelled 99.8 23 PDB header:protein transport
Chain: A: PDB Molecule:vacuolar protein sorting-associating protein 4b;
PDBTitle: crystal structure of mouse skd1/vps4b apo-form
31c1nsfA_



not modelled 99.8 24 PDB header:protein transport
Chain: A: PDB Molecule:n-ethylmaleimide sensitive factor;
PDBTitle: d2 hexamerization domain of n-ethylmaleimide sensitive factor (nsf)
32c1in8A_



not modelled 99.8 26 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
33d1d2na_



not modelled 99.8 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
34c2x8aA_



not modelled 99.8 22 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
35c2ce7B_



not modelled 99.8 26 PDB header:cell division protein
Chain: B: PDB Molecule:cell division protein ftsh;
PDBTitle: edta treated
36d1ixza_



not modelled 99.7 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
37d2ce7a2



not modelled 99.7 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
38c3nbxX_



not modelled 99.7 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
39c2c9oC_



not modelled 99.7 23 PDB header:hydrolase
Chain: C: PDB Molecule:ruvb-like 1;
PDBTitle: 3d structure of the human ruvb-like helicase ruvbl1
40d1r7ra3



not modelled 99.7 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
41d1e32a2



not modelled 99.7 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
42d1in4a2



not modelled 99.7 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
43c2r65A_



not modelled 99.7 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
44c1iy2A_



not modelled 99.7 26 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent metalloprotease ftsh;
PDBTitle: crystal structure of the ftsh atpase domain from thermus2 thermophilus
45d1ixsb2



not modelled 99.7 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
46c3k1jA_



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
47c2qz4A_



not modelled 99.7 24 PDB header:hydrolase
Chain: A: PDB Molecule:paraplegin;
PDBTitle: human paraplegin, aaa domain in complex with adp
48d1l8qa2



not modelled 99.7 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
49c1hqcB_



not modelled 99.7 24 PDB header:hydrolase
Chain: B: PDB Molecule:ruvb;
PDBTitle: structure of ruvb from thermus thermophilus hb8
50d1lv7a_



not modelled 99.6 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
51c3u5zM_



not modelled 99.6 19 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
52c2hcbC_



not modelled 99.6 18 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
53c2chgB_



not modelled 99.6 21 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
54c1xxhB_



not modelled 99.6 29 PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii subunit gamma;
PDBTitle: atpgs bound e. coli clamp loader complex
55d1jbka_



not modelled 99.6 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
56c1sxjA_



not modelled 99.5 16 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)
57d1sxjb2



not modelled 99.5 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
58d1w5sa2



not modelled 99.5 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
59d1sxje2



not modelled 99.5 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
60d1r6bx2



not modelled 99.5 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
61d1iqpa2



not modelled 99.5 28 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
62d1sxja2



not modelled 99.5 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
63c3f8tA_



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
64d1gvnb_



not modelled 99.5 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Plasmid maintenance system epsilon/zeta, toxin zeta subunit
65c1sxjB_



not modelled 99.5 21 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)
66c1sxjC_



not modelled 99.5 21 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)
67c1sxjE_



not modelled 99.5 19 PDB header:replication
Chain: E: 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)
68d1qvra2



not modelled 99.5 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
69c2chvE_



not modelled 99.5 24 PDB header:dna-binding protein
Chain: E: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c adpnp complex
70c1sxjD_



not modelled 99.5 26 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)
71c2p5tD_



not modelled 99.4 14 PDB header:transcription regulator
Chain: D: PDB Molecule:pezt;
PDBTitle: molecular and structural characterization of the pezat chromosomal2 toxin-antitoxin system of the human pathogen streptococcus pneumoniae
72c3bosA_



not modelled 99.4 20 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
73d1sxjc2



not modelled 99.4 21 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
74c1iqpF_



not modelled 99.4 27 PDB header:replication
Chain: F: PDB Molecule:rfcs;
PDBTitle: crystal structure of the clamp loader small subunit from2 pyrococcus furiosus
75d1njfa_



not modelled 99.4 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
76d1oz4a3



not modelled 99.4 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
77c2z4rB_



not modelled 99.4 22 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
78d1fnna2



not modelled 99.4 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
79c2p65A_



not modelled 99.4 25 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
80d1a5ta2



not modelled 99.4 19 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
81c1jr3E_



not modelled 99.3 22 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
82c3te6A_



not modelled 99.3 21 PDB header:gene regulation
Chain: A: PDB Molecule:regulatory protein sir3;
PDBTitle: crystal structure of the s. cerevisiae sir3 aaa+ domain
83d1sxjd2



not modelled 99.3 22 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
84c3pxgA_



not modelled 99.2 26 PDB header:protein binding
Chain: A: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca121 and clpc1-485 complex
85c3f9vA_



not modelled 99.2 17 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
86c3co5B_



not modelled 99.1 22 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
87c1fnnB_



not modelled 99.1 15 PDB header:cell cycle
Chain: B: PDB Molecule:cell division control protein 6;
PDBTitle: crystal structure of cdc6p from pyrobaculum aerophilum
88c2qbyB_



not modelled 99.0 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)
89c2v1uA_



not modelled 99.0 24 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
90c3ec2A_



not modelled 98.9 17 PDB header:replication
Chain: A: PDB Molecule:dna replication protein dnac;
PDBTitle: crystal structure of the dnac helicase loader
91c2ds8A_



98.9 100 PDB header:metal binding protein, protein binding
Chain: A: PDB Molecule:atp-dependent clp protease atp-binding subunit
PDBTitle: structure of the zbd-xb complex
92c1w5sB_



not modelled 98.9 21 PDB header:replication
Chain: B: PDB Molecule:origin recognition complex subunit 2 orc2;
PDBTitle: structure of the aeropyrum pernix orc2 protein (adp form)
93c2qbyA_



not modelled 98.8 19 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)
94d2gnoa2



not modelled 98.8 20 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
95c2w58B_



not modelled 98.7 16 PDB header:hydrolase
Chain: B: PDB Molecule:primosome component (helicase loader);
PDBTitle: crystal structure of the dnai
96c2kjqA_



not modelled 98.7 16 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.
97d2ds5a1



98.7 100 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:ClpX chaperone zinc binding domain
98c1ovxB_



98.7 100 PDB header:metal binding protein
Chain: B: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: nmr structure of the e. coli clpx chaperone zinc binding domain dimer
99c3qmzA_



not modelled 98.4 17 PDB header:motor protein
Chain: A: PDB Molecule:cytoplasmic dynein heavy chain;
PDBTitle: crystal structure of the cytoplasmic dynein heavy chain motor domain
100d1kaga_



not modelled 98.3 42 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Shikimate kinase (AroK)
101d1lw7a2



not modelled 98.3 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
102d1ye8a1



not modelled 98.3 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
103c3trfB_



not modelled 98.3 41 PDB header:transferase
Chain: B: PDB Molecule:shikimate kinase;
PDBTitle: structure of a shikimate kinase (arok) from coxiella burnetii
104c2gxaA_



not modelled 98.3 13 PDB header:replication/dna
Chain: A: PDB Molecule:replication protein e1;
PDBTitle: crystal structure of papillomavirus e1 hexameric helicase2 with ssdna and mgadp
105c3be4A_



not modelled 98.2 30 PDB header:transferase
Chain: A: PDB Molecule:adenylate kinase;
PDBTitle: crystal structure of cryptosporidium parvum adenylate kinase cgd5_3360
106c3tlxA_



not modelled 98.2 18 PDB header:transferase
Chain: A: PDB Molecule:adenylate kinase 2;
PDBTitle: crystal structure of pf10_0086, adenylate kinase from plasmodium2 falciparum
107d2iyva1



not modelled 98.2 35 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Shikimate kinase (AroK)
108d1svma_



not modelled 98.2 25 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
109c2qgzA_



not modelled 98.2 19 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
110c1zuiA_



not modelled 98.2 38 PDB header:transferase
Chain: A: PDB Molecule:shikimate kinase;
PDBTitle: structural basis for shikimate-binding specificity of helicobacter2 pylori shikimate kinase
111d1e6ca_



not modelled 98.1 33 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Shikimate kinase (AroK)
112d1viaa_



not modelled 98.1 50 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Shikimate kinase (AroK)
113c2og2A_



not modelled 98.1 23 PDB header:protein transport
Chain: A: PDB Molecule:putative signal recognition particle receptor;
PDBTitle: crystal structure of chloroplast ftsy from arabidopsis2 thaliana
114c1lw7A_



not modelled 98.1 14 PDB header:transferase
Chain: A: PDB Molecule:transcriptional regulator nadr;
PDBTitle: nadr protein from haemophilus influenzae
115c2ak3B_



not modelled 98.1 16 PDB header:transferase (phosphotransferase)
Chain: B: PDB Molecule:adenylate kinase isoenzyme-3;
PDBTitle: the three-dimensional structure of the complex between2 mitochondrial matrix adenylate kinase and its substrate3 amp at 1.85 angstroms resolution
116d1qhxa_



not modelled 98.1 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Chloramphenicol phosphotransferase
117d2ak3a1



not modelled 98.1 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nucleotide and nucleoside kinases
118d2i3ba1



not modelled 98.1 38 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
119c2iy3A_



not modelled 98.1 15 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
120c2ar7A_



not modelled 98.1 23 PDB header:transferase
Chain: A: PDB Molecule:adenylate kinase 4;
PDBTitle: crystal structure of human adenylate kinase 4, ak4

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