Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AES6
DateThu Jan 5 11:24:06 GMT 2012
Unique Job ID722f501f08c2a3c1

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3nuhB_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage: 44%
353 residues ( 44% 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.
732 residues ( 91%) 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  MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEII
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   .........70.........80.........90.........100.........110.........120
Sequence  VTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGV
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??????????
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   .........130.........140.........150.........160.........170.........180
Sequence  SVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVT
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   .........190.........200.........210.........220.........230.........240
Sequence  EFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNI
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   .........250.........260.........270.........280.........290.........300
Sequence  FYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKE
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?
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   .........310.........320.........330.........340.........350.........360
Sequence  GYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEY
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   .........370.........380.........390.........400.........410.........420
Sequence  LLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSEL
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   .........430.........440.........450.........460.........470.........480
Sequence  YLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGR
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??
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   .........490.........500.........510.........520.........530.........540
Sequence  DEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKG
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   .........550.........560.........570.........580.........590.........600
Sequence  KQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERR
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   .........610.........620.........630.........640.........650.........660
Sequence  YPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLF
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   .........670.........680.........690.........700.........710.........720
Sequence  EPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFE
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   .........730.........740.........750.........760.........770.........780
Sequence  QALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTL
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   .........790.........800....
Sequence  MGDAVEPRRAFIEENALKAANIDI
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??????
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Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

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

RankAligned region

PDB 3nuh chain B

3D model

Region: 402 - 783
Aligned: 353
Modelled: 379
Confidence: 100.0%
Identity: 98%
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 3lnu chain A

3D model

Region: 15 - 382
Aligned: 342
Modelled: 346
Confidence: 100.0%
Identity: 36%
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 - 387
Aligned: 347
Modelled: 364
Confidence: 100.0%
Identity: 23%
PDB header:isomerase
Chain: B: PDB Molecule:dna topoisomerase ii, alpha isozyme;
PDBTitle: human dna topoisomerase iia atpase/adp

Phyre2

PDB 1ei1 chain B

3D model

Region: 2 - 392
Aligned: 391
Modelled: 391
Confidence: 100.0%
Identity: 99%
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 1qzr chain A

3D model

Region: 7 - 384
Aligned: 348
Modelled: 378
Confidence: 100.0%
Identity: 27%
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 1s16 chain B

3D model

Region: 4 - 385
Aligned: 376
Modelled: 380
Confidence: 100.0%
Identity: 37%
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 3cwv chain B

3D model

Region: 16 - 374
Aligned: 307
Modelled: 317
Confidence: 100.0%
Identity: 31%
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 1kij chain B

3D model

Region: 9 - 392
Aligned: 382
Modelled: 384
Confidence: 100.0%
Identity: 47%
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 2xkj chain E

3D model

Region: 393 - 795
Aligned: 231
Modelled: 234
Confidence: 100.0%
Identity: 47%
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 2xcq chain A

3D model

Region: 400 - 769
Aligned: 190
Modelled: 198
Confidence: 100.0%
Identity: 71%
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: 406 - 799
Aligned: 190
Modelled: 191
Confidence: 100.0%
Identity: 71%
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 3fof chain D

3D model

Region: 411 - 795
Aligned: 197
Modelled: 213
Confidence: 100.0%
Identity: 66%
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 2zjt chain B

3D model

Region: 413 - 781
Aligned: 183
Modelled: 205
Confidence: 100.0%
Identity: 57%
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 - 213
Aligned: 206
Modelled: 207
Confidence: 100.0%
Identity: 28%
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 1bjt chain A

3D model

Region: 394 - 752
Aligned: 177
Modelled: 190
Confidence: 100.0%
Identity: 34%
Fold: Type II DNA topoisomerase
Superfamily: Type II DNA topoisomerase
Family: Type II DNA topoisomerase

Phyre2

PDB 1bjt chain A

3D model

Region: 394 - 752
Aligned: 177
Modelled: 190
Confidence: 100.0%
Identity: 34%
PDB header:topoisomerase
Chain: A: PDB Molecule:topoisomerase ii;
PDBTitle: topoisomerase ii residues 409-1201

Phyre2

PDB 3qx3 chain B

3D model

Region: 399 - 538
Aligned: 139
Modelled: 140
Confidence: 100.0%
Identity: 35%
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 1ei1 chain A domain 2

3D model

Region: 2 - 220
Aligned: 219
Modelled: 219
Confidence: 100.0%
Identity: 99%
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 - 219
Aligned: 211
Modelled: 216
Confidence: 100.0%
Identity: 47%
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 - 220
Aligned: 210
Modelled: 212
Confidence: 100.0%
Identity: 51%
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

c3nuhB_
2

c3lnuA_
3

c1zxnB_
4

c1ei1B_
5

c1qzrA_
6

c1s16B_
7

c3cwvB_
8

c1kijB_
9

c2xkjE_
10

c2xcqA_
11

c2xcsD_
12

c3fofD_
13

c2zjtB_
14

d1pvga2
15

d1bjta_
16

c1bjtA_
17

c3qx3B_
18

d1ei1a2
19

d1s16a2
20

d1kija2
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3nuhB_



100.0 98 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
2c3lnuA_



100.0 36 PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit b;
PDBTitle: crystal structure of pare subunit
3c1zxnB_



100.0 23 PDB header:isomerase
Chain: B: PDB Molecule:dna topoisomerase ii, alpha isozyme;
PDBTitle: human dna topoisomerase iia atpase/adp
4c1ei1B_



100.0 99 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
5c1qzrA_



100.0 27 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)
6c1s16B_



100.0 37 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
7c3cwvB_



100.0 31 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
8c1kijB_



100.0 47 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
9c2xkjE_



100.0 47 PDB header:isomerase
Chain: E: PDB Molecule:topoisomerase iv;
PDBTitle: crystal structure of catalytic core of a. baumannii topo iv2 (pare-parc fusion truncate)
10c2xcqA_



100.0 71 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
11c2xcsD_



100.0 71 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
12c3fofD_



100.0 66 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
13c2zjtB_



100.0 57 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
14d1pvga2



100.0 28 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
15d1bjta_



100.0 34 Fold:Type II DNA topoisomerase
Superfamily:Type II DNA topoisomerase
Family:Type II DNA topoisomerase
16c1bjtA_



100.0 34 PDB header:topoisomerase
Chain: A: PDB Molecule:topoisomerase ii;
PDBTitle: topoisomerase ii residues 409-1201
17c3qx3B_



100.0 35 PDB header:isomerase/dna/isomerase inhibitor
Chain: B: PDB Molecule:dna topoisomerase 2-beta;
PDBTitle: human topoisomerase iibeta in complex with dna and etoposide
18d1ei1a2



100.0 99 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 47 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 51 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
21d1kija1



not modelled 100.0 44 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
22d1ei1a1



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
23c3g7bB_



not modelled 100.0 57 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: staphylococcus aureus gyrase b co-complex with inhibitor
24d1s16a1



not modelled 100.0 24 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 44 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 23 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
27c2q2eB_



not modelled 99.9 20 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
28c2zbkB_



not modelled 99.8 19 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
29c3h4lB_



not modelled 99.8 17 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
30d2hkja3



not modelled 99.7 14 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
31c1mx0D_



not modelled 99.7 17 PDB header:isomerase
Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b;
PDBTitle: structure of topoisomerase subunit
32c3na3A_



not modelled 99.6 16 PDB header:protein binding
Chain: A: PDB Molecule:dna mismatch repair protein mlh1;
PDBTitle: mutl protein homolog 1 isoform 1 from homo sapiens
33d1b63a2



not modelled 99.5 20 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:DNA gyrase/MutL, N-terminal domain
34c1bknA_



not modelled 99.4 16 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 99.3 21 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 99.1 24 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 98.9 17 PDB header:chaperone
Chain: A: PDB Molecule:atp-dependent molecular chaperone hsp82;
PDBTitle: hsp90 delta24-n210 mutant
39c3iedA_



not modelled 98.8 23 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
40d2iwxa1



not modelled 98.7 18 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
41c2fwyA_



not modelled 98.7 19 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 98.7 18 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
43c1zwhA_



not modelled 98.7 18 PDB header:chaperone
Chain: A: PDB Molecule:atp-dependent molecular chaperone hsp82;
PDBTitle: yeast hsp82 in complex with the novel hsp90 inhibitor radester amine
44d1uyma_



not modelled 98.7 18 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
45c2cg9A_



not modelled 98.4 17 PDB header:chaperone
Chain: A: PDB Molecule:atp-dependent molecular chaperone hsp82;
PDBTitle: crystal structure of an hsp90-sba1 closed chaperone complex
46c2iorA_



not modelled 98.4 20 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
47d1qy5a_



not modelled 98.3 18 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
48d2gqpa1



not modelled 98.2 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
49c2o1wB_



not modelled 98.2 21 PDB header:chaperone
Chain: B: PDB Molecule:endoplasmin;
PDBTitle: structure of n-terminal plus middle domains (n+m) of grp94
50c3pehB_



not modelled 98.2 19 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
51c1y4sA_



not modelled 98.0 16 PDB header:chaperone
Chain: A: PDB Molecule:chaperone protein htpg;
PDBTitle: conformation rearrangement of heat shock protein 90 upon2 adp binding
52c1gjvA_



not modelled 97.8 22 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
53c2bu8A_



not modelled 97.8 26 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
54c1y8oA_



not modelled 97.7 21 PDB header:transferase
Chain: A: PDB Molecule:[pyruvate dehydrogenase [lipoamide]] kinase isozyme 3;
PDBTitle: crystal structure of the pdk3-l2 complex
55c2iopD_



not modelled 97.7 14 PDB header:chaperone
Chain: D: PDB Molecule:chaperone protein htpg;
PDBTitle: crystal structure of full-length htpg, the escherichia coli2 hsp90, bound to adp
56c3d2rB_



not modelled 97.7 22 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
57c2q8fA_



not modelled 97.4 25 PDB header:transferase
Chain: A: PDB Molecule:[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1;
PDBTitle: structure of pyruvate dehydrogenase kinase isoform 1
58c3d36B_



not modelled 97.2 19 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
59d1jm6a2



not modelled 97.1 23 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
60c2c2aA_



not modelled 97.1 18 PDB header:transferase
Chain: A: PDB Molecule:sensor histidine kinase;
PDBTitle: structure of the entire cytoplasmic portion of a sensor2 histidine kinase protein
61d1gkza2



not modelled 96.7 20 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
62c2o1uA_



not modelled 96.5 21 PDB header:chaperone
Chain: A: PDB Molecule:endoplasmin;
PDBTitle: structure of full length grp94 with amp-pnp bound
63c3a0rA_



not modelled 96.4 27 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)
64c1b3qA_



not modelled 96.3 28 PDB header:transferase
Chain: A: PDB Molecule:protein (chemotaxis protein chea);
PDBTitle: crystal structure of chea-289, a signal transducing histidine kinase
65d1th8a_



not modelled 96.2 17 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
66d1y8oa2



not modelled 96.1 23 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
67d1bxda_



not modelled 96.0 24 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
68c3a0tA_



not modelled 95.8 23 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)
69d2c2aa2



not modelled 95.8 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
70c2ch4A_



not modelled 95.7 32 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
71c3jz3B_



not modelled 95.2 36 PDB header:transferase
Chain: B: PDB Molecule:sensor protein qsec;
PDBTitle: structure of the cytoplasmic segment of histidine kinase qsec
72d1ysra1



not modelled 95.0 24 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
73c3ehgA_



not modelled 94.4 24 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
74d1id0a_



not modelled 94.3 31 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
75c3ke6A_



not modelled 92.4 28 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
76d1i58a_



not modelled 90.5 34 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
77d1ixma_



not modelled 89.8 9 Fold:Sporulation response regulatory protein Spo0B
Superfamily:Sporulation response regulatory protein Spo0B
Family:Sporulation response regulatory protein Spo0B
78c3gieA_



not modelled 86.7 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 85.1 32 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 80.6 39 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
81d1vdda_



not modelled 77.4 18 Fold:Recombination protein RecR
Superfamily:Recombination protein RecR
Family:Recombination protein RecR
82c3ssoE_



not modelled 64.3 38 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
83d2fcja1



not modelled 52.7 20 Fold:Toprim domain
Superfamily:Toprim domain
Family:Toprim domain
84c1vddC_



not modelled 51.4 20 PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr
85d2hkja2



not modelled 47.8 15 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
86c3dmaA_



not modelled 45.4 20 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
87c3ggqA_



not modelled 45.1 46 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
88c1yo8A_



not modelled 40.4 32 PDB header:cell adhesion
Chain: A: PDB Molecule:thrombospondin-2;
PDBTitle: structure of the c-terminal domain of human thrombospondin-2
89d1mw9x_



not modelled 39.7 27 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
90d1wvha1



not modelled 38.8 18 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Phosphotyrosine-binding domain (PTB)
91d1ecwa_



not modelled 34.6 42 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
92d1hiwa_



not modelled 34.5 42 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
93c3devB_



not modelled 34.3 24 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:sh1221;
PDBTitle: crystal structure of sh1221 protein from staphylococcus haemolyticus,2 northeast structural genomics consortium target shr87
94d2gola1



not modelled 34.1 42 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
95d1l6na1



not modelled 32.0 42 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
96d2dkqa1



not modelled 32.0 18 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Phosphotyrosine-binding domain (PTB)
97d1tama_



not modelled 30.5 29 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Immunodeficiency virus matrix proteins
98c2gajA_



not modelled 27.6 23 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form
99d1ddma_



not modelled 26.4 20 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Phosphotyrosine-binding domain (PTB)
100d1ux6a1



not modelled 26.2 35 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Thrombospondin C-terminal domain
101c1ux6A_



not modelled 26.1 35 PDB header:cell adhesion
Chain: A: PDB Molecule:thrombospondin-1;
PDBTitle: structure of a thrombospondin c-terminal fragment reveals a2 novel calcium core in the type 3 repeats
102d1i7da_



not modelled 25.6 20 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
103d1vkza1



not modelled 25.4 23 Fold:Barrel-sandwich hybrid
Superfamily:Rudiment single hybrid motif
Family:BC C-terminal domain-like
104c3bq9A_



not modelled 25.1 21 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted rossmann fold nucleotide-binding domain-
PDBTitle: crystal structure of predicted nucleotide-binding protein from2 idiomarina baltica os145
105d1gkub3



not modelled 24.1 29 Fold:Prokaryotic type I DNA topoisomerase
Superfamily:Prokaryotic type I DNA topoisomerase
Family:Prokaryotic type I DNA topoisomerase
106c1ir6A_



not modelled 23.9 24 PDB header:hydrolase
Chain: A: PDB Molecule:exonuclease recj;
PDBTitle: crystal structure of exonuclease recj bound to manganese
107d1ir6a_



not modelled 23.9 24 Fold:DHH phosphoesterases
Superfamily:DHH phosphoesterases
Family:Exonuclease RecJ
108c2ccaA_



not modelled 23.7 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:peroxidase/catalase t;
PDBTitle: crystal structure of the catalase-peroxidase (katg) and2 s315t mutant from mycobacterium tuberculosis
109d1h72c1



not modelled 23.6 18 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:GHMP Kinase, N-terminal domain
110c3fbyC_



not modelled 22.7 26 PDB header:cell adhesion
Chain: C: PDB Molecule:cartilage oligomeric matrix protein;
PDBTitle: the crystal structure of the signature domain of cartilage oligomeric2 matrix protein.
111c2o59B_



not modelled 22.3 21 PDB header:isomerase/dna
Chain: B: PDB Molecule:dna topoisomerase 3;
PDBTitle: structure of e. coli topoisomerase iii in complex with an 8-2 base single stranded oligonucleotide. frozen in glycerol3 ph 8.0
112d1jmca1



not modelled 22.1 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
113d1wj1a_



not modelled 21.2 18 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Phosphotyrosine-binding domain (PTB)
114d2idba2



not modelled 21.0 21 Fold:UbiD C-terminal domain-like
Superfamily:UbiD C-terminal domain-like
Family:UbiD C-terminal domain-like
115d1nuia1



not modelled 20.6 22 Fold:DNA primase core
Superfamily:DNA primase core
Family:Primase fragment of primase-helicase protein
116c1zc1A_



not modelled 20.4 23 PDB header:protein turnover
Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1;
PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites

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