Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP06993
DateThu Jan 5 10:59:50 GMT 2012
Unique Job IDfeb81367c89cf400

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3iytG_
Top template information
PDB header:apoptosis
Chain: G: PDB Molecule:apoptotic protease-activating factor 1;
PDBTitle: structure of an apoptosome-procaspase-9 card complex
Confidence and coverage
Confidence: 99.9% Coverage: 36%
321 residues ( 36% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
802 residues ( 89%) 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  MLIPSKLSRPVRLDHTVVRERLLAKLSGANNFRLALITSPAGYGKTTLISQWAAGKNDIG
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Disorder  ???????????????












































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   .........70.........80.........90.........100.........110.........120
Sequence  WYSLDEGDNQQERFASYLIAAVQQATNGHCAICETMAQKRQYASLTSLFAQLFIELAEWH
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?
????????????????

















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   .........130.........140.........150.........160.........170.........180
Sequence  SPLYLVIDDYHLITNPVIHESMRFFIRHQPENLTLVVLSRNLPQLGIANLRVRDQLLEIG
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??














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   .........190.........200.........210.........220.........230.........240
Sequence  SQQLAFTHQEAKQFFDCRLSSPIEAAESSRICDDVSGWATALQLIALSARQNTHSAHKSA
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   .........250.........260.........270.........280.........290.........300
Sequence  RRLAGINASHLSDYLVDEVLDNVDLATRHFLLKSAILRSMNDALITRVTGEENGQMRLEE
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Disorder 
??
??
?



















































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   .........310.........320.........330.........340.........350.........360
Sequence  IERQGLFLQRMDDTGEWFCYHPLFGNFLRQRCQWELAAELPEIHRAAAESWMAQGFPSEA
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??
























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   .........370.........380.........390.........400.........410.........420
Sequence  IHHALAAGDALMLRDILLNHAWSLFNHSELSLLEESLKALPWDSLLENPQLVLLQAWLMQ
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   .........430.........440.........450.........460.........470.........480
Sequence  SQHRYGEVNTLLARAEHEIKDIREDTMHAEFNALRAQVAINDGNPDEAERLAKLALEELP
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??




































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   .........490.........500.........510.........520.........530.........540
Sequence  PGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFA
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   .........550.........560.........570.........580.........590.........600
Sequence  QGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVL
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?




































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   .........610.........620.........630.........640.........650.........660
Sequence  SSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYW
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   .........670.........680.........690.........700.........710.........720
Sequence  QMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARS
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   .........730.........740.........750.........760.........770.........780
Sequence  LRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEAMAQQLRQ
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   .........790.........800.........810.........820.........830.........840
Sequence  LIQLNTLPELEQHRAQRILREINQHHRHKFAHFDENFVERLLNHPEVPELIRTSPLTQRE
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??????????????????


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   .........850.........860.........870.........880.........890.........900
Sequence  WQVLGLIYSGYSNEQIAGELEVAATTIKTHIRNLYQKLGVAHRQDAVQHAQQLLKMMGYG
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?
??????
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   .
Sequence  V
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 3iyt chain G

3D model

Region: 9 - 350
Aligned: 321
Modelled: 336
Confidence: 99.9%
Identity: 13%
PDB header:apoptosis
Chain: G: PDB Molecule:apoptotic protease-activating factor 1;
PDBTitle: structure of an apoptosome-procaspase-9 card complex

Phyre2

PDB 1z6t chain C

3D model

Region: 8 - 334
Aligned: 306
Modelled: 327
Confidence: 99.9%
Identity: 14%
PDB header:apoptosis
Chain: C: PDB Molecule:apoptotic protease activating factor 1;
PDBTitle: structure of the apoptotic protease-activating factor 12 bound to adp

Phyre2

PDB 2q0o chain A

3D model

Region: 827 - 896
Aligned: 70
Modelled: 70
Confidence: 99.9%
Identity: 19%
PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing

Phyre2

PDB 3szt chain B

3D model

Region: 829 - 896
Aligned: 68
Modelled: 68
Confidence: 99.9%
Identity: 25%
PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone

Phyre2

PDB 1h0m chain D

3D model

Region: 814 - 896
Aligned: 83
Modelled: 83
Confidence: 99.9%
Identity: 17%
PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna

Phyre2

PDB 1hz4 chain A

3D model

Region: 439 - 802
Aligned: 364
Modelled: 364
Confidence: 99.9%
Identity: 100%
Fold: alpha-alpha superhelix
Superfamily: TPR-like
Family: Transcription factor MalT domain III

Phyre2

PDB 3qp5 chain C

3D model

Region: 834 - 895
Aligned: 62
Modelled: 62
Confidence: 99.9%
Identity: 29%
PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)

Phyre2

PDB 2a5y chain B

3D model

Region: 8 - 332
Aligned: 303
Modelled: 313
Confidence: 99.8%
Identity: 13%
PDB header:apoptosis
Chain: B: PDB Molecule:ced-4;
PDBTitle: structure of a ced-4/ced-9 complex

Phyre2

PDB 2fna chain A

3D model

Region: 7 - 231
Aligned: 222
Modelled: 221
Confidence: 99.8%
Identity: 11%
PDB header:atp-binding protein
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of an archaeal aaa+ atpase (sso1545) from sulfolobus2 solfataricus p2 at 2.00 a resolution

Phyre2

PDB 2qen chain A

3D model

Region: 1 - 329
Aligned: 321
Modelled: 329
Confidence: 99.8%
Identity: 13%
PDB header:unknown function
Chain: A: PDB Molecule:walker-type atpase;
PDBTitle: the walker-type atpase paby2304 of pyrococcus abyssi

Phyre2

PDB 2fna chain A domain 2

3D model

Region: 7 - 271
Aligned: 251
Modelled: 252
Confidence: 99.8%
Identity: 13%
Fold: P-loop containing nucleoside triphosphate hydrolases
Superfamily: P-loop containing nucleoside triphosphate hydrolases
Family: Extended AAA-ATPase domain

Phyre2

PDB 1zlj chain E

3D model

Region: 832 - 896
Aligned: 65
Modelled: 65
Confidence: 99.8%
Identity: 35%
PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain

Phyre2

PDB 3c3w chain B

3D model

Region: 830 - 893
Aligned: 64
Modelled: 64
Confidence: 99.8%
Identity: 36%
PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr

Phyre2

PDB 3clo chain C

3D model

Region: 836 - 896
Aligned: 61
Modelled: 61
Confidence: 99.8%
Identity: 30%
PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution

Phyre2

PDB 2krf chain B

3D model

Region: 828 - 896
Aligned: 69
Modelled: 69
Confidence: 99.8%
Identity: 26%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a

Phyre2

PDB 3kln chain C

3D model

Region: 793 - 892
Aligned: 100
Modelled: 100
Confidence: 99.8%
Identity: 26%
PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst

Phyre2

PDB 1p4w chain A

3D model

Region: 828 - 896
Aligned: 69
Modelled: 69
Confidence: 99.8%
Identity: 22%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 1l3l chain A domain 1

3D model

Region: 832 - 896
Aligned: 65
Modelled: 65
Confidence: 99.8%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 1fse chain A

3D model

Region: 834 - 897
Aligned: 64
Modelled: 64
Confidence: 99.7%
Identity: 34%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: C-terminal effector domain of the bipartite response regulators
Family: GerE-like (LuxR/UhpA family of transcriptional regulators)

Phyre2

PDB 1rnl chain A

3D model

Region: 836 - 895
Aligned: 60
Modelled: 60
Confidence: 99.7%
Identity: 32%
PDB header:signal transduction protein
Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl;
PDBTitle: the nitrate/nitrite response regulator protein narl from narl

Phyre2
1

c3iytG_
2

c1z6tC_
3

c2q0oA_
4

c3sztB_
5

c1h0mD_
6

d1hz4a_
7

c3qp5C_
8

c2a5yB_
9

c2fnaA_
10

c2qenA_
11

d2fnaa2
12

c1zljE_
13

c3c3wB_
14

c3cloC_
15

c2krfB_
16

c3klnC_
17

d1p4wa_
18

d1l3la1
19

d1fsea_
20

c1rnlA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3iytG_



99.9 13 PDB header:apoptosis
Chain: G: PDB Molecule:apoptotic protease-activating factor 1;
PDBTitle: structure of an apoptosome-procaspase-9 card complex
2c1z6tC_



99.9 14 PDB header:apoptosis
Chain: C: PDB Molecule:apoptotic protease activating factor 1;
PDBTitle: structure of the apoptotic protease-activating factor 12 bound to adp
3c2q0oA_



99.9 19 PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
4c3sztB_



99.9 25 PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone
5c1h0mD_



99.9 17 PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna
6d1hz4a_



99.9 100 Fold:alpha-alpha superhelix
Superfamily:TPR-like
Family:Transcription factor MalT domain III
7c3qp5C_



99.9 29 PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
8c2a5yB_



99.8 13 PDB header:apoptosis
Chain: B: PDB Molecule:ced-4;
PDBTitle: structure of a ced-4/ced-9 complex
9c2fnaA_



99.8 11 PDB header:atp-binding protein
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of an archaeal aaa+ atpase (sso1545) from sulfolobus2 solfataricus p2 at 2.00 a resolution
10c2qenA_



99.8 13 PDB header:unknown function
Chain: A: PDB Molecule:walker-type atpase;
PDBTitle: the walker-type atpase paby2304 of pyrococcus abyssi
11d2fnaa2



99.8 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
12c1zljE_



99.8 35 PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
13c3c3wB_



99.8 36 PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
14c3cloC_



99.8 30 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution
15c2krfB_



99.8 26 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
16c3klnC_



99.8 26 PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
17d1p4wa_



99.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
18d1l3la1



99.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
19d1fsea_



99.7 34 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
20c1rnlA_



99.7 32 PDB header:signal transduction protein
Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl;
PDBTitle: the nitrate/nitrite response regulator protein narl from narl
21c2rnjA_



not modelled 99.7 40 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
22d1a04a1



not modelled 99.7 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
23c1zn2A_



not modelled 99.7 45 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
24c1x3uA_



not modelled 99.7 28 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
25c2jpcA_



not modelled 99.7 34 PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
26c1fnnB_



not modelled 99.7 17 PDB header:cell cycle
Chain: B: PDB Molecule:cell division control protein 6;
PDBTitle: crystal structure of cdc6p from pyrobaculum aerophilum
27c2qbyB_



not modelled 99.7 10 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)
28d1yioa1



not modelled 99.7 45 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
29c2v1uA_



not modelled 99.7 18 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
30c2qbyA_



not modelled 99.6 12 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)
31d1fnna2



not modelled 99.4 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
32c1w5sB_



not modelled 99.4 15 PDB header:replication
Chain: B: PDB Molecule:origin recognition complex subunit 2 orc2;
PDBTitle: structure of the aeropyrum pernix orc2 protein (adp form)
33c1in8A_



not modelled 99.3 22 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction dna helicase ruvb;
PDBTitle: thermotoga maritima ruvb t158v
34c2chgB_



not modelled 99.2 12 PDB header:dna-binding protein
Chain: B: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c domains 1 and 2
35c3pvsA_



not modelled 99.1 16 PDB header:recombination
Chain: A: PDB Molecule:replication-associated recombination protein a;
PDBTitle: structure and biochemical activities of escherichia coli mgsa
36c1sxjC_



not modelled 99.1 18 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)
37c3pfiB_



not modelled 99.1 18 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
38c2chvE_



not modelled 99.1 13 PDB header:dna-binding protein
Chain: E: PDB Molecule:replication factor c small subunit;
PDBTitle: replication factor c adpnp complex
39d1w5sa2



not modelled 99.1 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
40d1sxjd2



not modelled 99.0 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
41d1in4a2



not modelled 99.0 26 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
42c3te6A_



not modelled 99.0 12 PDB header:gene regulation
Chain: A: PDB Molecule:regulatory protein sir3;
PDBTitle: crystal structure of the s. cerevisiae sir3 aaa+ domain
43d1iqpa2



not modelled 99.0 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
44c1iqpF_



not modelled 99.0 14 PDB header:replication
Chain: F: PDB Molecule:rfcs;
PDBTitle: crystal structure of the clamp loader small subunit from2 pyrococcus furiosus
45d1sxjc2



not modelled 99.0 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
46d1sxjb2



not modelled 99.0 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
47d1r6bx2



not modelled 99.0 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
48c1hqcB_



not modelled 98.9 22 PDB header:hydrolase
Chain: B: PDB Molecule:ruvb;
PDBTitle: structure of ruvb from thermus thermophilus hb8
49c1sxjB_



not modelled 98.9 18 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)
50c3u5zM_



not modelled 98.9 11 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
51d1njfa_



not modelled 98.9 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
52c1xwiA_



not modelled 98.9 16 PDB header:protein transport
Chain: A: PDB Molecule:skd1 protein;
PDBTitle: crystal structure of vps4b
53c2ce7B_



not modelled 98.9 17 PDB header:cell division protein
Chain: B: PDB Molecule:cell division protein ftsh;
PDBTitle: edta treated
54d1sxja2



not modelled 98.9 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
55c1sxjA_



not modelled 98.9 13 PDB header:replication
Chain: A: PDB Molecule:activator 1 95 kda subunit;
PDBTitle: crystal structure of the eukaryotic clamp loader2 (replication factor c, rfc) bound to the dna sliding clamp3 (proliferating cell nuclear antigen, pcna)
56d1a5ta2



not modelled 98.9 10 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
57c3d8bB_



not modelled 98.9 17 PDB header:hydrolase
Chain: B: PDB Molecule:fidgetin-like protein 1;
PDBTitle: crystal structure of human fidgetin-like protein 1 in complex with adp
58c1sxjD_



not modelled 98.9 12 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)
59c1xxhB_



not modelled 98.9 14 PDB header:transferase
Chain: B: PDB Molecule:dna polymerase iii subunit gamma;
PDBTitle: atpgs bound e. coli clamp loader complex
60c1sxjE_



not modelled 98.9 13 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)
61d1sxje2



not modelled 98.9 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
62d1qvra2



not modelled 98.9 12 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
63d1ixsb2



not modelled 98.9 23 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
64c3b9pA_



not modelled 98.8 18 PDB header:hydrolase
Chain: A: PDB Molecule:cg5977-pa, isoform a;
PDBTitle: spastin
65c3bosA_



not modelled 98.8 13 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
66c2zamA_



not modelled 98.8 18 PDB header:protein transport
Chain: A: PDB Molecule:vacuolar protein sorting-associating protein 4b;
PDBTitle: crystal structure of mouse skd1/vps4b apo-form
67c1r6bX_



not modelled 98.8 12 PDB header:hydrolase
Chain: X: PDB Molecule:clpa protein;
PDBTitle: high resolution crystal structure of clpa
68c2dhrC_



not modelled 98.7 16 PDB header:hydrolase
Chain: C: PDB Molecule:ftsh;
PDBTitle: whole cytosolic region of atp-dependent metalloprotease2 ftsh (g399l)
69c1kgsA_



not modelled 98.7 21 PDB header:dna binding protein
Chain: A: PDB Molecule:dna binding response regulator d;
PDBTitle: crystal structure at 1.50 a of an ompr/phob homolog from thermotoga2 maritima
70d1jbka_



not modelled 98.7 14 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
71c2z4rB_



not modelled 98.7 13 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
72c3hu2C_



not modelled 98.7 15 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
73d1ixza_



not modelled 98.6 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
74c3h4mC_



not modelled 98.6 17 PDB header:hydrolase
Chain: C: PDB Molecule:proteasome-activating nucleotidase;
PDBTitle: aaa atpase domain of the proteasome- activating nucleotidase
75c1jr3E_



not modelled 98.6 11 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
76d2ce7a2



not modelled 98.6 17 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
77c1iy2A_



not modelled 98.6 16 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent metalloprotease ftsh;
PDBTitle: crystal structure of the ftsh atpase domain from thermus2 thermophilus
78c2qz4A_



not modelled 98.5 17 PDB header:hydrolase
Chain: A: PDB Molecule:paraplegin;
PDBTitle: human paraplegin, aaa domain in complex with adp
79c1qvrB_



not modelled 98.5 25 PDB header:chaperone
Chain: B: PDB Molecule:clpb protein;
PDBTitle: crystal structure analysis of clpb
80d1r7ra3



not modelled 98.5 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
81c2p65A_



not modelled 98.5 15 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
82c3pxgA_



not modelled 98.5 12 PDB header:protein binding
Chain: A: PDB Molecule:negative regulator of genetic competence clpc/mecb;
PDBTitle: structure of meca121 and clpc1-485 complex
83c2c9oC_



not modelled 98.5 11 PDB header:hydrolase
Chain: C: PDB Molecule:ruvb-like 1;
PDBTitle: 3d structure of the human ruvb-like helicase ruvbl1
84c3eihB_



not modelled 98.5 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
85d1l8qa2



not modelled 98.5 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
86c2r65A_



not modelled 98.5 16 PDB header:hydrolase
Chain: A: PDB Molecule:cell division protease ftsh homolog;
PDBTitle: crystal structure of helicobacter pylori atp dependent protease, ftsh2 adp complex
87c3cf1C_



not modelled 98.4 15 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
88d1ttya_



not modelled 98.4 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
89c2kjqA_



not modelled 98.4 17 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.
90c3q9sA_



not modelled 98.4 28 PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding response regulator;
PDBTitle: crystal structure of rra(1-215) from deinococcus radiodurans
91d1e32a2



not modelled 98.4 16 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
92c1s3sA_



not modelled 98.4 14 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
93c3gw4B_



not modelled 98.4 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of uncharacterized protein from deinococcus2 radiodurans. northeast structural genomics consortium target drr162b.
94d1smyf2



not modelled 98.3 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
95d2p7vb1



not modelled 98.3 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
96d1r6bx3



not modelled 98.3 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
97c3nbxX_



not modelled 98.2 14 PDB header:hydrolase
Chain: X: PDB Molecule:atpase rava;
PDBTitle: crystal structure of e. coli rava (regulatory atpase variant a) in2 complex with adp
98d1rp3a2



not modelled 98.2 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
99c3hteC_



not modelled 98.2 17 PDB header:motor protein
Chain: C: PDB Molecule:atp-dependent clp protease atp-binding subunit clpx;
PDBTitle: crystal structure of nucleotide-free hexameric clpx
100c2x8aA_



not modelled 98.2 13 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
101c3hugA_



not modelled 98.2 30 PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
102d1or7a1



not modelled 98.2 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
103c2o8xA_



not modelled 98.1 22 PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
104c1ny5A_



not modelled 98.1 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigm54 activator (aaa+ atpase) in the inactive2 state
105d1xsva_



not modelled 98.1 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
106d1ku7a_



not modelled 98.1 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
107d1d2na_



not modelled 98.1 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
108c2hcbC_



not modelled 98.1 11 PDB header:replication
Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of amppcp-bound dnaa from aquifex aeolicus
109d1ny5a2



not modelled 98.1 15 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
110d1lv7a_



not modelled 98.1 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
111c3ulqA_



not modelled 98.1 9 PDB header:gene regulation/transcription activator
Chain: A: PDB Molecule:response regulator aspartate phosphatase f;
PDBTitle: crystal structure of the anti-activator rapf complexed with the2 response regulator coma dna binding domain
112c2ifuA_



not modelled 98.0 8 PDB header:endocytosis/exocytosis
Chain: A: PDB Molecule:gamma-snap;
PDBTitle: crystal structure of a gamma-snap from danio rerio
113c1nsfA_



not modelled 98.0 15 PDB header:protein transport
Chain: A: PDB Molecule:n-ethylmaleimide sensitive factor;
PDBTitle: d2 hexamerization domain of n-ethylmaleimide sensitive factor (nsf)
114d1g41a_



not modelled 98.0 13 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
115d1ku3a_



not modelled 98.0 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
116c1rp3G_



not modelled 98.0 26 PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm
117c3mzyA_



not modelled 98.0 28 PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
118c3sf4B_



not modelled 98.0 11 PDB header:signaling protein/protein binding
Chain: B: PDB Molecule:g-protein-signaling modulator 2;
PDBTitle: crystal structure of the complex between the conserved cell polarity2 proteins inscuteable and lgn
119c1ojlF_



not modelled 97.9 15 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
120d1s7oa_



not modelled 97.9 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like

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