Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP20083
DateThu Jan 5 11:37:45 GMT 2012
Unique Job IDfe384c2ce170588e

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3lnuA_
Top template information
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit b;
PDBTitle: crystal structure of pare subunit
Confidence and coverage
Confidence:100.0% Coverage: 55%
344 residues ( 55% 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.
619 residues ( 98%) 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  MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILH
Secondary structure 
SS confidence 
Disorder  ??????
?
???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVN
Secondary structure 
SS confidence 
Disorder 
?????????????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  ALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFS
Secondary structure 
SS confidence 
Disorder 
????
?
?
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  VSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIG
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  NFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFCEYRNI
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  LPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWLNQ
Secondary structure 
SS confidence 
Disorder  ?????
?
?
?
?
??
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  NVQAAELLAEMAISSAQRRMRAAKKVVRKKLTSGPALPGKLADCTAQDLNRTELFLVEGD
Secondary structure 
SS confidence 
Disorder 
??????????????
??
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  SAGGSAKQARDREYQAIMPLKGKILNTWEVSSDEVLASQEVHDISVAIGIDPDSDDLSQL
Secondary structure 
SS confidence 
Disorder 
?
?
????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  RYGKICILADADSDGLHIATLLCALFVKHFRALVKHGHVYVALPPLYRIDLGKEVYYALT
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  EEEKEGVLEQLKRKKGKPNVQRFKGLGEMNPMQLRETTLDPNTRRLVQLTIDDEDDQRTD
Secondary structure 
SS confidence 
Disorder 
?
????
?
?
Disorder confidence 
 
   .........610.........620.........630
Sequence  AMMDMLLAKKRSEDRRNWLQEKGDMAEIEV
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 3lnu chain A

3D model

Region: 15 - 379
Aligned: 344
Modelled: 345
Confidence: 100.0%
Identity: 61%
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit b;
PDBTitle: crystal structure of pare subunit

Phyre2

PDB 1zxn chain B

3D model

Region: 7 - 383
Aligned: 343
Modelled: 365
Confidence: 100.0%
Identity: 17%
PDB header:isomerase
Chain: B: PDB Molecule:dna topoisomerase ii, alpha isozyme;
PDBTitle: human dna topoisomerase iia atpase/adp

Phyre2

PDB 1s16 chain B

3D model

Region: 4 - 383
Aligned: 380
Modelled: 380
Confidence: 100.0%
Identity: 100%
PDB header:isomerase
Chain: B: PDB Molecule:topoisomerase iv subunit b;
PDBTitle: crystal structure of e. coli topoisomerase iv pare 43kda subunit2 complexed with adpnp

Phyre2

PDB 1qzr chain A

3D model

Region: 7 - 381
Aligned: 349
Modelled: 365
Confidence: 100.0%
Identity: 23%
PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase ii;
PDBTitle: crystal structure of the atpase region of saccharomyces cerevisiae2 topoisomerase ii bound to icrf-187 (dexrazoxane)

Phyre2

PDB 1ei1 chain B

3D model

Region: 2 - 385
Aligned: 381
Modelled: 384
Confidence: 100.0%
Identity: 36%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase b;
PDBTitle: dimerization of e. coli dna gyrase b provides a structural mechanism2 for activating the atpase catalytic center

Phyre2

PDB 2xkj chain E

3D model

Region: 387 - 629
Aligned: 239
Modelled: 243
Confidence: 100.0%
Identity: 71%
PDB header:isomerase
Chain: E: PDB Molecule:topoisomerase iv;
PDBTitle: crystal structure of catalytic core of a. baumannii topo iv2 (pare-parc fusion truncate)

Phyre2

PDB 1kij chain B

3D model

Region: 9 - 385
Aligned: 376
Modelled: 377
Confidence: 100.0%
Identity: 39%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: crystal structure of the 43k atpase domain of thermus thermophilus2 gyrase b in complex with novobiocin

Phyre2

PDB 3cwv chain B

3D model

Region: 16 - 371
Aligned: 304
Modelled: 314
Confidence: 100.0%
Identity: 28%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase, b subunit, truncated;
PDBTitle: crystal structure of b-subunit of the dna gyrase from myxococcus2 xanthus

Phyre2

PDB 2xcq chain A

3D model

Region: 394 - 593
Aligned: 189
Modelled: 200
Confidence: 100.0%
Identity: 48%
PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit b, dna gyrase subunit a;
PDBTitle: the 2.98a crystal structure of the catalytic core (b'a'2 region) of staphylococcus aureus dna gyrase

Phyre2

PDB 2xcs chain D

3D model

Region: 400 - 630
Aligned: 193
Modelled: 196
Confidence: 100.0%
Identity: 45%
PDB header:isomerase
Chain: D: PDB Molecule:dna gyrase subunit b, dna gyrase subunit a;
PDBTitle: the 2.1a crystal structure of s. aureus gyrase complex with gsk2994232 and dna

Phyre2

PDB 1bjt chain A

3D model

Region: 387 - 627
Aligned: 204
Modelled: 216
Confidence: 100.0%
Identity: 25%
Fold: Type II DNA topoisomerase
Superfamily: Type II DNA topoisomerase
Family: Type II DNA topoisomerase

Phyre2

PDB 1bjt chain A

3D model

Region: 387 - 627
Aligned: 204
Modelled: 216
Confidence: 100.0%
Identity: 25%
PDB header:topoisomerase
Chain: A: PDB Molecule:topoisomerase ii;
PDBTitle: topoisomerase ii residues 409-1201

Phyre2

PDB 3fof chain D

3D model

Region: 405 - 622
Aligned: 197
Modelled: 218
Confidence: 100.0%
Identity: 47%
PDB header:isomerase/dna
Chain: D: PDB Molecule:dna topoisomerase 4 subunit b;
PDBTitle: structural insight into the quinolone-dna cleavage complex2 of type iia topoisomerases

Phyre2

PDB 3nuh chain B

3D model

Region: 396 - 609
Aligned: 188
Modelled: 211
Confidence: 100.0%
Identity: 55%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: a domain insertion in e. coli gyrb adopts a novel fold that plays a2 critical role in gyrase function

Phyre2

PDB 3qx3 chain B

3D model

Region: 389 - 629
Aligned: 191
Modelled: 196
Confidence: 100.0%
Identity: 32%
PDB header:isomerase/dna/isomerase inhibitor
Chain: B: PDB Molecule:dna topoisomerase 2-beta;
PDBTitle: human topoisomerase iibeta in complex with dna and etoposide

Phyre2

PDB 2zjt chain B

3D model

Region: 407 - 607
Aligned: 178
Modelled: 201
Confidence: 100.0%
Identity: 44%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: crystal structure of dna gyrase b' domain sheds lights on2 the mechanism for t-segment navigation

Phyre2

PDB 1pvg chain A domain 2

3D model

Region: 7 - 210
Aligned: 204
Modelled: 204
Confidence: 100.0%
Identity: 24%
Fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family: DNA gyrase/MutL, N-terminal domain

Phyre2

PDB 1ei1 chain A domain 2

3D model

Region: 2 - 217
Aligned: 214
Modelled: 216
Confidence: 100.0%
Identity: 46%
Fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family: DNA gyrase/MutL, N-terminal domain

Phyre2

PDB 1s16 chain A domain 2

3D model

Region: 4 - 216
Aligned: 213
Modelled: 213
Confidence: 100.0%
Identity: 100%
Fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family: DNA gyrase/MutL, N-terminal domain

Phyre2

PDB 1kij chain A domain 2

3D model

Region: 9 - 217
Aligned: 209
Modelled: 209
Confidence: 100.0%
Identity: 49%
Fold: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family: DNA gyrase/MutL, N-terminal domain

Phyre2
1
c3lnuA_
2
c1zxnB_
3
c1s16B_
4
c1qzrA_
5
c1ei1B_
6
c2xkjE_
7
c1kijB_
8
c3cwvB_
9
c2xcqA_
10
c2xcsD_
11
d1bjta_
12
c1bjtA_
13
c3fofD_
14
c3nuhB_
15
c3qx3B_
16
c2zjtB_
17
d1pvga2
18
d1ei1a2
19
d1s16a2
20
d1kija2
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
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42
43
44
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69
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73
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75
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84
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94
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103
104
105



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3lnuA_
100.0 61 PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit b;
PDBTitle: crystal structure of pare subunit
2c1zxnB_
100.0 17 PDB header:isomerase
Chain: B: PDB Molecule:dna topoisomerase ii, alpha isozyme;
PDBTitle: human dna topoisomerase iia atpase/adp
3c1s16B_
100.0 100 PDB header:isomerase
Chain: B: PDB Molecule:topoisomerase iv subunit b;
PDBTitle: crystal structure of e. coli topoisomerase iv pare 43kda subunit2 complexed with adpnp
4c1qzrA_
100.0 23 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase ii;
PDBTitle: crystal structure of the atpase region of saccharomyces cerevisiae2 topoisomerase ii bound to icrf-187 (dexrazoxane)
5c1ei1B_
100.0 36 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase b;
PDBTitle: dimerization of e. coli dna gyrase b provides a structural mechanism2 for activating the atpase catalytic center
6c2xkjE_
100.0 71 PDB header:isomerase
Chain: E: PDB Molecule:topoisomerase iv;
PDBTitle: crystal structure of catalytic core of a. baumannii topo iv2 (pare-parc fusion truncate)
7c1kijB_
100.0 39 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: crystal structure of the 43k atpase domain of thermus thermophilus2 gyrase b in complex with novobiocin
8c3cwvB_
100.0 28 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase, b subunit, truncated;
PDBTitle: crystal structure of b-subunit of the dna gyrase from myxococcus2 xanthus
9c2xcqA_
100.0 48 PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit b, dna gyrase subunit a;
PDBTitle: the 2.98a crystal structure of the catalytic core (b'a'2 region) of staphylococcus aureus dna gyrase
10c2xcsD_
100.0 45 PDB header:isomerase
Chain: D: PDB Molecule:dna gyrase subunit b, dna gyrase subunit a;
PDBTitle: the 2.1a crystal structure of s. aureus gyrase complex with gsk2994232 and dna
11d1bjta_
100.0 25 Fold:Type II DNA topoisomerase
Superfamily:Type II DNA topoisomerase
Family:Type II DNA topoisomerase
12c1bjtA_
100.0 25 PDB header:topoisomerase
Chain: A: PDB Molecule:topoisomerase ii;
PDBTitle: topoisomerase ii residues 409-1201
13c3fofD_
100.0 47 PDB header:isomerase/dna
Chain: D: PDB Molecule:dna topoisomerase 4 subunit b;
PDBTitle: structural insight into the quinolone-dna cleavage complex2 of type iia topoisomerases
14c3nuhB_
100.0 55 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: a domain insertion in e. coli gyrb adopts a novel fold that plays a2 critical role in gyrase function
15c3qx3B_
100.0 32 PDB header:isomerase/dna/isomerase inhibitor
Chain: B: PDB Molecule:dna topoisomerase 2-beta;
PDBTitle: human topoisomerase iibeta in complex with dna and etoposide
16c2zjtB_
100.0 44 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: crystal structure of dna gyrase b' domain sheds lights on2 the mechanism for t-segment navigation
17d1pvga2
100.0 24 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
18d1ei1a2
100.0 46 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
19d1s16a2
100.0 100 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
20d1kija2
100.0 49 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
21c3g7bB_
not modelled 100.0 45 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: staphylococcus aureus gyrase b co-complex with inhibitor
22d1s16a1
not modelled 100.0 100 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
23d1kija1
not modelled 100.0 28 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
24d1ei1a1
not modelled 100.0 23 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
25d1s14a_
not modelled 100.0 100 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
26d1pvga1
not modelled 100.0 21 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
27c2q2eB_
not modelled 99.8 14 PDB header:isomerase
Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b;
PDBTitle: crystal structure of the topoisomerase vi holoenzyme from2 methanosarcina mazei
28c3h4lB_
not modelled 99.8 18 PDB header:dna binding protein, protein binding
Chain: B: PDB Molecule:dna mismatch repair protein pms1;
PDBTitle: crystal structure of n terminal domain of a dna repair protein
29c2zbkB_
not modelled 99.8 20 PDB header:isomerase
Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b;
PDBTitle: crystal structure of an intact type ii dna topoisomerase:2 insights into dna transfer mechanisms
30c1mx0D_
not modelled 99.8 24 PDB header:isomerase
Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b;
PDBTitle: structure of topoisomerase subunit
31d2hkja3
not modelled 99.7 22 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
32d1b63a2
not modelled 99.6 22 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
33c3na3A_
not modelled 99.6 19 PDB header:protein binding
Chain: A: PDB Molecule:dna mismatch repair protein mlh1;
PDBTitle: mutl protein homolog 1 isoform 1 from homo sapiens
34c1bknA_
not modelled 99.5 18 PDB header:dna repair
Chain: A: PDB Molecule:mutl;
PDBTitle: crystal structure of an n-terminal 40kd fragment of e. coli2 dna mismatch repair protein mutl
35d1h7sa2
not modelled 99.4 20 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
36d1bkna2
not modelled 99.4 22 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
37c1ea6A_
not modelled 99.3 25 PDB header:dna repair
Chain: A: PDB Molecule:pms1 protein homolog 2;
PDBTitle: n-terminal 40kda fragment of nhpms2 complexed with adp
38c2akpA_
not modelled 99.2 21 PDB header:chaperone
Chain: A: PDB Molecule:atp-dependent molecular chaperone hsp82;
PDBTitle: hsp90 delta24-n210 mutant
39d2iwxa1
not modelled 99.0 22 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Heat shock protein 90, HSP90, N-terminal domain
40c1zwhA_
not modelled 98.9 22 PDB header:chaperone
Chain: A: PDB Molecule:atp-dependent molecular chaperone hsp82;
PDBTitle: yeast hsp82 in complex with the novel hsp90 inhibitor radester amine
41c2fwyA_
not modelled 98.9 21 PDB header:chaperone
Chain: A: PDB Molecule:heat shock protein hsp 90-alpha;
PDBTitle: structure of human hsp90-alpha bound to the potent water2 soluble inhibitor pu-h64
42d1uyla_
not modelled 98.9 21 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Heat shock protein 90, HSP90, N-terminal domain
43c3iedA_
not modelled 98.9 25 PDB header:chaperone
Chain: A: PDB Molecule:heat shock protein;
PDBTitle: crystal structure of n-terminal domain of plasmodium falciparum hsp902 (pf14_0417) in complex with amppn
44c2o1wB_
not modelled 98.8 17 PDB header:chaperone
Chain: B: PDB Molecule:endoplasmin;
PDBTitle: structure of n-terminal plus middle domains (n+m) of grp94
45d1uyma_
not modelled 98.7 19 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Heat shock protein 90, HSP90, N-terminal domain
46c2iorA_
not modelled 98.7 24 PDB header:chaperone
Chain: A: PDB Molecule:chaperone protein htpg;
PDBTitle: crystal structure of the n-terminal domain of htpg, the2 escherichia coli hsp90, bound to adp
47c3pehB_
not modelled 98.6 16 PDB header:chaperone
Chain: B: PDB Molecule:endoplasmin homolog;
PDBTitle: crystal structure of the n-terminal domain of an hsp90 from plasmodium2 falciparum, pfl1070c in the presence of a thienopyrimidine derivative
48d1qy5a_
not modelled 98.6 20 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Heat shock protein 90, HSP90, N-terminal domain
49c1y4sA_
not modelled 98.6 23 PDB header:chaperone
Chain: A: PDB Molecule:chaperone protein htpg;
PDBTitle: conformation rearrangement of heat shock protein 90 upon2 adp binding
50d2gqpa1
not modelled 98.5 20 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Heat shock protein 90, HSP90, N-terminal domain
51c2cg9A_
not modelled 98.5 19 PDB header:chaperone
Chain: A: PDB Molecule:atp-dependent molecular chaperone hsp82;
PDBTitle: crystal structure of an hsp90-sba1 closed chaperone complex
52c2bu8A_
not modelled 98.2 16 PDB header:transferase
Chain: A: PDB Molecule:pyruvate dehydrogenase kinase isoenzyme 2;
PDBTitle: crystal structures of human pyruvate dehydrogenase kinase 22 containing physiological and synthetic ligands
53c3d2rB_
not modelled 98.2 17 PDB header:transferase
Chain: B: PDB Molecule:[pyruvate dehydrogenase [lipoamide]] kinase isozyme 4;
PDBTitle: crystal structure of pyruvate dehydrogenase kinase isoform 4 in2 complex with adp
54c2q8fA_
not modelled 98.1 14 PDB header:transferase
Chain: A: PDB Molecule:[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1;
PDBTitle: structure of pyruvate dehydrogenase kinase isoform 1
55c2iopD_
not modelled 98.1 22 PDB header:chaperone
Chain: D: PDB Molecule:chaperone protein htpg;
PDBTitle: crystal structure of full-length htpg, the escherichia coli2 hsp90, bound to adp
56c1y8oA_
not modelled 98.0 13 PDB header:transferase
Chain: A: PDB Molecule:[pyruvate dehydrogenase [lipoamide]] kinase isozyme 3;
PDBTitle: crystal structure of the pdk3-l2 complex
57c1gjvA_
not modelled 98.0 12 PDB header:transferase
Chain: A: PDB Molecule:[3-methyl-2-oxobutanoate dehydrogenase
PDBTitle: branched-chain alpha-ketoacid dehydrogenase kinase (bck)2 complxed with atp-gamma-s
58d1jm6a2
not modelled 97.6 17 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:alpha-ketoacid dehydrogenase kinase, C-terminal domain
59c3d36B_
not modelled 97.5 18 PDB header:transferase/transferase inhibitor
Chain: B: PDB Molecule:sporulation kinase b;
PDBTitle: how to switch off a histidine kinase: crystal structure of2 geobacillus stearothermophilus kinb with the inhibitor sda
60c2c2aA_
not modelled 97.4 21 PDB header:transferase
Chain: A: PDB Molecule:sensor histidine kinase;
PDBTitle: structure of the entire cytoplasmic portion of a sensor2 histidine kinase protein
61c2o1uA_
not modelled 97.4 17 PDB header:chaperone
Chain: A: PDB Molecule:endoplasmin;
PDBTitle: structure of full length grp94 with amp-pnp bound
62d1gkza2
not modelled 97.2 15 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:alpha-ketoacid dehydrogenase kinase, C-terminal domain
63c2ch4A_
not modelled 97.2 25 PDB header:transferase/chemotaxis
Chain: A: PDB Molecule:chemotaxis protein chea;
PDBTitle: complex between bacterial chemotaxis histidine kinase chea2 domains p4 and p5 and receptor-adaptor protein chew
64d1th8a_
not modelled 97.1 18 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
65c1b3qA_
not modelled 96.7 18 PDB header:transferase
Chain: A: PDB Molecule:protein (chemotaxis protein chea);
PDBTitle: crystal structure of chea-289, a signal transducing histidine kinase
66d2c2aa2
not modelled 96.5 21 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
67d1y8oa2
not modelled 96.5 25 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:alpha-ketoacid dehydrogenase kinase, C-terminal domain
68c3a0rA_
not modelled 96.3 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)
69c3a0tA_
not modelled 96.3 15 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: catalytic domain of histidine kinase thka (tm1359) in2 complex with adp and mg ion (trigonal)
70d1bxda_
not modelled 96.0 14 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
71d1i58a_
not modelled 95.9 23 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
72c3jz3B_
not modelled 95.8 32 PDB header:transferase
Chain: B: PDB Molecule:sensor protein qsec;
PDBTitle: structure of the cytoplasmic segment of histidine kinase qsec
73d1ysra1
not modelled 95.7 21 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
74d1id0a_
not modelled 95.7 22 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
75c3ehgA_
not modelled 95.5 22 PDB header:transferase
Chain: A: PDB Molecule:sensor kinase (yocf protein);
PDBTitle: crystal structure of the atp-binding domain of desk in complex with2 atp
76c3ke6A_
not modelled 95.0 31 PDB header:unknown function
Chain: A: PDB Molecule:protein rv1364c/mt1410;
PDBTitle: the crystal structure of the rsbu and rsbw domains of rv1364c from2 mycobacterium tuberculosis
77d1ixma_
not modelled 93.4 11 Fold:Sporulation response regulatory protein Spo0B
Superfamily:Sporulation response regulatory protein Spo0B
Family:Sporulation response regulatory protein Spo0B
78c3gieA_
not modelled 92.4 22 PDB header:transferase
Chain: A: PDB Molecule:sensor histidine kinase desk;
PDBTitle: crystal structure of deskc_h188e in complex with amp-pcp
79c3zxqA_
not modelled 91.3 29 PDB header:transferase
Chain: A: PDB Molecule:hypoxia sensor histidine kinase response regulator dost;
PDBTitle: crystal structure of the atp-binding domain of mycobacterium2 tuberculosis dost
80c3zxoB_
not modelled 87.5 37 PDB header:transferase
Chain: B: PDB Molecule:redox sensor histidine kinase response regulator devs;
PDBTitle: crystal structure of the mutant atp-binding domain of2 mycobacterium tuberculosis doss
81c3ssoE_
not modelled 76.6 34 PDB header:transferase
Chain: E: PDB Molecule:methyltransferase;
PDBTitle: myce methyltransferase from the mycinamycin biosynthetic pathway in2 complex with mg and sah, crystal form 2
82d1mw9x_
not modelled 75.5 20 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
83d2fcja1
not modelled 69.8 22 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
84c2gajA_
not modelled 54.4 21 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form
85c3ggqA_
not modelled 48.6 40 PDB header:viral protein
Chain: A: PDB Molecule:capsid protein;
PDBTitle: dimerization of hepatitis e virus capsid protein e2s domain is2 essential for virus-host interaction
86d1r62a_
not modelled 48.4 14 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
87d2hkja2
not modelled 43.0 13 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
88d1ecwa_
not modelled 37.3 43 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
89c3dmaA_
not modelled 36.0 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:exopolyphosphatase-related protein;
PDBTitle: crystal structure of an exopolyphosphatase-related protein2 from bacteroides fragilis. northeast structural genomics3 target bfr192
90d1hiwa_
not modelled 35.6 43 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
91d1x87a_
not modelled 35.5 12 Fold:Urocanase
Superfamily:Urocanase
Family:Urocanase
92d2gola1
not modelled 34.7 43 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
93d1tama_
not modelled 33.8 46 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
94d1l6na1
not modelled 33.3 46 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
95d1jmca1
not modelled 33.2 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
96d1h72c1
not modelled 32.4 14 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:GHMP Kinase, N-terminal domain
97c3lmmA_
not modelled 31.7 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35
98d1gkub3
not modelled 30.3 23 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
99d1uwka_
not modelled 29.5 9 Fold:Urocanase
Superfamily:Urocanase
Family:Urocanase
100c3fm2A_
not modelled 29.4 22 PDB header:heme-binding protein
Chain: A: PDB Molecule:uncharacterized protein, distantly related to a heme
PDBTitle: crystal structure of a putative heme-binding protein (ava_4353) from2 anabaena variabilis atcc 29413 at 1.80 a resolution
101c2fknC_
not modelled 25.4 9 PDB header:lyase
Chain: C: PDB Molecule:urocanate hydratase;
PDBTitle: crystal structure of urocanase from bacillus subtilis
102d2jdid1
not modelled 23.7 15 Fold:Left-handed superhelix
Superfamily:C-terminal domain of alpha and beta subunits of F1 ATP synthase
Family:C-terminal domain of alpha and beta subunits of F1 ATP synthase
103c1nuiA_
not modelled 22.5 23 PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein
104d1i7da_
not modelled 22.3 16 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
105d1k92a2
not modelled 21.6 28 Fold:Argininosuccinate synthetase, C-terminal domain
Superfamily:Argininosuccinate synthetase, C-terminal domain
Family:Argininosuccinate synthetase, C-terminal domain

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