Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AES4
DateThu Jan 5 11:24:06 GMT 2012
Unique Job ID8a01775cad7e4659

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1zvuA_
Top template information
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit a;
PDBTitle: structure of the full-length e. coli parc subunit
Confidence and coverage
Confidence:100.0% Coverage: 76%
669 residues ( 76% 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.
760 residues ( 87%) 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  MSDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWN
Secondary structure 
SS confidence 
Disorder  ??????
?
????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  KAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAM
Secondary structure 
SS confidence 
Disorder  ???
?????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  RYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMAT
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  NIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKV
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  YIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDG
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  MRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRRE
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  VVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNV
Secondary structure 
SS confidence 
Disorder 
?
?????????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  AAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE
Secondary structure 
SS confidence 
Disorder  ??????????????????????????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  LLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVV
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  VTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVY
Secondary structure 
SS confidence 
Disorder 
????????????????????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  SMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVL
Secondary structure 
SS confidence 
Disorder 
????????
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  TEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTG
Secondary structure 
SS confidence 
Disorder  ?
???????
?????????
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  VRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERN
Secondary structure 
SS confidence 
Disorder 
?
?
????
?
??
Disorder confidence 
 
   .........790.........800.........810.........820.........830.........840
Sequence  GLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVA
Secondary structure 
SS confidence 
Disorder 
??????
??
?
Disorder confidence 
 
   .........850.........860.........870.....
Sequence  EPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE
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 1zvu chain A

3D model

Region: 31 - 784
Aligned: 669
Modelled: 695
Confidence: 100.0%
Identity: 36%
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit a;
PDBTitle: structure of the full-length e. coli parc subunit

Phyre2

PDB 2wl2 chain B

3D model

Region: 13 - 522
Aligned: 506
Modelled: 510
Confidence: 100.0%
Identity: 99%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit a;
PDBTitle: crystal structure of n-terminal domain of gyra with the2 antibiotic simocyclinone d8

Phyre2

PDB 2xcs chain D

3D model

Region: 9 - 522
Aligned: 479
Modelled: 480
Confidence: 100.0%
Identity: 60%
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 3ifz chain A

3D model

Region: 2 - 522
Aligned: 482
Modelled: 487
Confidence: 100.0%
Identity: 52%
PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: crystal structure of the first part of the mycobacterium tuberculosis2 dna gyrase reaction core: the breakage and reunion domain at 2.7 a3 resolution

Phyre2

PDB 1ab4 chain A

3D model

Region: 30 - 522
Aligned: 477
Modelled: 487
Confidence: 100.0%
Identity: 98%
Fold: Type II DNA topoisomerase
Superfamily: Type II DNA topoisomerase
Family: Type II DNA topoisomerase

Phyre2

PDB 2xcq chain A

3D model

Region: 1 - 522
Aligned: 474
Modelled: 488
Confidence: 100.0%
Identity: 60%
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 3ilw chain A

3D model

Region: 30 - 523
Aligned: 459
Modelled: 460
Confidence: 100.0%
Identity: 51%
PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: structure of dna gyrase subunit a n-terminal domain

Phyre2

PDB 2xkj chain E

3D model

Region: 9 - 530
Aligned: 479
Modelled: 488
Confidence: 100.0%
Identity: 41%
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 2inr chain A

3D model

Region: 33 - 527
Aligned: 442
Modelled: 461
Confidence: 100.0%
Identity: 50%
PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase 4 subunit a;
PDBTitle: crystal structure of a 59 kda fragment of topoisomerase iv subunit a2 (grla) from staphylococcus aureus

Phyre2

PDB 2nov chain D

3D model

Region: 33 - 521
Aligned: 440
Modelled: 453
Confidence: 100.0%
Identity: 47%
PDB header:isomerase
Chain: D: PDB Molecule:dna topoisomerase 4 subunit a;
PDBTitle: breakage-reunion domain of s.pneumoniae topo iv: crystal2 structure of a gram-positive quinolone target

Phyre2

PDB 3qx3 chain B

3D model

Region: 3 - 516
Aligned: 449
Modelled: 480
Confidence: 100.0%
Identity: 25%
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 1bjt chain A

3D model

Region: 12 - 517
Aligned: 458
Modelled: 486
Confidence: 100.0%
Identity: 21%
PDB header:topoisomerase
Chain: A: PDB Molecule:topoisomerase ii;
PDBTitle: topoisomerase ii residues 409-1201

Phyre2

PDB 1bjt chain A

3D model

Region: 12 - 517
Aligned: 458
Modelled: 486
Confidence: 100.0%
Identity: 21%
Fold: Type II DNA topoisomerase
Superfamily: Type II DNA topoisomerase
Family: Type II DNA topoisomerase

Phyre2

PDB 3l6v chain A

3D model

Region: 532 - 843
Aligned: 312
Modelled: 312
Confidence: 100.0%
Identity: 59%
PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: crystal structure of the xanthomonas campestris gyrase a c-2 terminal domain

Phyre2

PDB 1wp5 chain A

3D model

Region: 534 - 849
Aligned: 311
Modelled: 316
Confidence: 100.0%
Identity: 31%
Fold: 6-bladed beta-propeller
Superfamily: GyrA/ParC C-terminal domain-like
Family: GyrA/ParC C-terminal domain-like

Phyre2

PDB 1suu chain A

3D model

Region: 537 - 839
Aligned: 291
Modelled: 303
Confidence: 100.0%
Identity: 28%
Fold: 6-bladed beta-propeller
Superfamily: GyrA/ParC C-terminal domain-like
Family: GyrA/ParC C-terminal domain-like

Phyre2

PDB 1zi0 chain A

3D model

Region: 536 - 841
Aligned: 286
Modelled: 286
Confidence: 100.0%
Identity: 99%
PDB header:isomerase, dna bindng protein
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: a superhelical spiral in escherichia coli dna gyrase a c-2 terminal domain imparts unidirectional supercoiling bias

Phyre2

PDB 3no0 chain B

3D model

Region: 539 - 841
Aligned: 272
Modelled: 287
Confidence: 100.0%
Identity: 24%
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit a;
PDBTitle: aquifex aeolicus type iia topoisomerase c-terminal domain

Phyre2

PDB 1zvt chain A

3D model

Region: 536 - 788
Aligned: 237
Modelled: 253
Confidence: 100.0%
Identity: 18%
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit a;
PDBTitle: structure of the e. coli parc c-terminal domain

Phyre2

PDB 3ku8 chain A

3D model

Region: 363 - 496
Aligned: 134
Modelled: 134
Confidence: 100.0%
Identity: 100%
PDB header:toxin/isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: ccdbvfi:gyra14ec

Phyre2
1
c1zvuA_
2
c2wl2B_
3
c2xcsD_
4
c3ifzA_
5
d1ab4a_
6
c2xcqA_
7
c3ilwA_
8
c2xkjE_
9
c2inrA_
10
c2novD_
11
c3qx3B_
12
c1bjtA_
13
d1bjta_
14
c3l6vA_
15
d1wp5a_
16
d1suua_
17
c1zi0A_
18
c3no0B_
19
c1zvtA_
20
c3ku8A_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1zvuA_
100.0 36 PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit a;
PDBTitle: structure of the full-length e. coli parc subunit
2c2wl2B_
100.0 99 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit a;
PDBTitle: crystal structure of n-terminal domain of gyra with the2 antibiotic simocyclinone d8
3c2xcsD_
100.0 60 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
4c3ifzA_
100.0 52 PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: crystal structure of the first part of the mycobacterium tuberculosis2 dna gyrase reaction core: the breakage and reunion domain at 2.7 a3 resolution
5d1ab4a_
100.0 98 Fold:Type II DNA topoisomerase
Superfamily:Type II DNA topoisomerase
Family:Type II DNA topoisomerase
6c2xcqA_
100.0 60 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
7c3ilwA_
100.0 51 PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: structure of dna gyrase subunit a n-terminal domain
8c2xkjE_
100.0 41 PDB header:isomerase
Chain: E: PDB Molecule:topoisomerase iv;
PDBTitle: crystal structure of catalytic core of a. baumannii topo iv2 (pare-parc fusion truncate)
9c2inrA_
100.0 50 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase 4 subunit a;
PDBTitle: crystal structure of a 59 kda fragment of topoisomerase iv subunit a2 (grla) from staphylococcus aureus
10c2novD_
100.0 47 PDB header:isomerase
Chain: D: PDB Molecule:dna topoisomerase 4 subunit a;
PDBTitle: breakage-reunion domain of s.pneumoniae topo iv: crystal2 structure of a gram-positive quinolone target
11c3qx3B_
100.0 25 PDB header:isomerase/dna/isomerase inhibitor
Chain: B: PDB Molecule:dna topoisomerase 2-beta;
PDBTitle: human topoisomerase iibeta in complex with dna and etoposide
12c1bjtA_
100.0 21 PDB header:topoisomerase
Chain: A: PDB Molecule:topoisomerase ii;
PDBTitle: topoisomerase ii residues 409-1201
13d1bjta_
100.0 21 Fold:Type II DNA topoisomerase
Superfamily:Type II DNA topoisomerase
Family:Type II DNA topoisomerase
14c3l6vA_
100.0 59 PDB header:isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: crystal structure of the xanthomonas campestris gyrase a c-2 terminal domain
15d1wp5a_
100.0 31 Fold:6-bladed beta-propeller
Superfamily:GyrA/ParC C-terminal domain-like
Family:GyrA/ParC C-terminal domain-like
16d1suua_
100.0 28 Fold:6-bladed beta-propeller
Superfamily:GyrA/ParC C-terminal domain-like
Family:GyrA/ParC C-terminal domain-like
17c1zi0A_
100.0 99 PDB header:isomerase, dna bindng protein
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: a superhelical spiral in escherichia coli dna gyrase a c-2 terminal domain imparts unidirectional supercoiling bias
18c3no0B_
100.0 24 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit a;
PDBTitle: aquifex aeolicus type iia topoisomerase c-terminal domain
19c1zvtA_
100.0 18 PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase iv subunit a;
PDBTitle: structure of the e. coli parc c-terminal domain
20c3ku8A_
100.0 100 PDB header:toxin/isomerase
Chain: A: PDB Molecule:dna gyrase subunit a;
PDBTitle: ccdbvfi:gyra14ec
21d1x75a1
not modelled 100.0 94 Fold:Type II DNA topoisomerase
Superfamily:Type II DNA topoisomerase
Family:Type II DNA topoisomerase
22c2oajA_
not modelled 86.9 12 PDB header:endocytosis/exocytosis
Chain: A: PDB Molecule:protein sni1;
PDBTitle: crystal structure of sro7 from s. cerevisiae
23c3dm0A_
not modelled 73.6 15 PDB header:sugar binding protein,signaling protein
Chain: A: PDB Molecule:maltose-binding periplasmic protein fused with
PDBTitle: maltose binding protein fusion with rack1 from a. thaliana
24c1t3jA_
not modelled 72.3 25 PDB header:membrane protein
Chain: A: PDB Molecule:mitofusin 1;
PDBTitle: mitofusin domain hr2 v686m/i708m mutant
25c2q6tB_
not modelled 61.6 24 PDB header:hydrolase
Chain: B: PDB Molecule:dnab replication fork helicase;
PDBTitle: crystal structure of the thermus aquaticus dnab monomer
26c3jroA_
not modelled 58.2 13 PDB header:transport protein, structural protein
Chain: A: PDB Molecule:fusion protein of protein transport protein sec13
PDBTitle: nup84-nup145c-sec13 edge element of the npc lattice
27c1c9lA_
not modelled 56.3 13 PDB header:endocytosis/exocytosis
Chain: A: PDB Molecule:clathrin;
PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin
28d2g0da1
not modelled 56.2 16 Fold:alpha/alpha toroid
Superfamily:LanC-like
Family:LanC-like
29d1jwea_
not modelled 54.0 16 Fold:N-terminal domain of DnaB helicase
Superfamily:N-terminal domain of DnaB helicase
Family:N-terminal domain of DnaB helicase
30c3fokH_
not modelled 53.6 17 PDB header:structural genomics, unknown function
Chain: H: PDB Molecule:uncharacterized protein cgl0159;
PDBTitle: crystal structure of cgl0159 from corynebacterium2 glutamicum (brevibacterium flavum). northeast structural3 genomics target cgr115
31c3a7pB_
not modelled 53.5 15 PDB header:protein transport
Chain: B: PDB Molecule:autophagy protein 16;
PDBTitle: the crystal structure of saccharomyces cerevisiae atg16
32c2vyeA_
not modelled 50.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: crystal structure of the dnac-ssdna complex
33c3lssA_
not modelled 48.2 14 PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: trypanosoma brucei seryl-trna synthetase in complex with atp
34d2v8qb1
not modelled 47.9 22 Fold:AMPKBI-like
Superfamily:AMPKBI-like
Family:AMPKBI-like
35c1q1hA_
not modelled 40.7 28 PDB header:transcription
Chain: A: PDB Molecule:transcription factor e;
PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha
36d1q1ha_
not modelled 40.7 28 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcription factor E/IIe-alpha, N-terminal domain
37c3gndC_
not modelled 38.8 14 PDB header:lyase
Chain: C: PDB Molecule:aldolase lsrf;
PDBTitle: crystal structure of e. coli lsrf in complex with ribulose-5-phosphate
38d1b79a_
not modelled 35.4 17 Fold:N-terminal domain of DnaB helicase
Superfamily:N-terminal domain of DnaB helicase
Family:N-terminal domain of DnaB helicase
39c1dpuA_
not modelled 35.3 36 PDB header:dna binding protein
Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain;
PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88)
40d1dpua_
not modelled 35.3 36 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:C-terminal domain of RPA32
41d2ayua1
not modelled 34.1 15 Fold:NAP-like
Superfamily:NAP-like
Family:NAP-like
42c2ayuA_
not modelled 34.1 15 PDB header:chaperone
Chain: A: PDB Molecule:nucleosome assembly protein;
PDBTitle: the structure of nucleosome assembly protein suggests a mechanism for2 histone binding and shuttling
43c2qjhH_
not modelled 33.8 19 PDB header:lyase
Chain: H: PDB Molecule:putative aldolase mj0400;
PDBTitle: m. jannaschii adh synthase covalently bound to2 dihydroxyacetone phosphate
44c3mkqA_
not modelled 33.5 12 PDB header:transport protein
Chain: A: PDB Molecule:coatomer beta'-subunit;
PDBTitle: crystal structure of yeast alpha/betaprime-cop subcomplex of the copi2 vesicular coat
45c3a7mA_
not modelled 29.6 13 PDB header:gene regulation, chaperone
Chain: A: PDB Molecule:flagellar protein flit;
PDBTitle: structure of flit, the flagellar type iii chaperone for flid
46d2qrdb1
not modelled 29.1 15 Fold:AMPKBI-like
Superfamily:AMPKBI-like
Family:AMPKBI-like
47c2h47F_
not modelled 28.6 10 PDB header:oxidoreductase/electron transport
Chain: F: PDB Molecule:aromatic amine dehydrogenase;
PDBTitle: crystal structure of an electron transfer complex between2 aromatic amine dephydrogenase and azurin from alcaligenes3 faecalis (form 1)
48c2jesG_
not modelled 28.4 12 PDB header:viral protein
Chain: G: PDB Molecule:portal protein;
PDBTitle: portal protein from bacteriophage spp1
49c2b5nD_
not modelled 28.0 12 PDB header:dna binding protein/protein binding
Chain: D: PDB Molecule:damage-specific dna binding protein 1;
PDBTitle: crystal structure of the ddb1 bpb domain
50d2dloa1
not modelled 27.5 71 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
51d1ivsa1
not modelled 27.3 27 Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Valyl-tRNA synthetase (ValRS) C-terminal domain
52c1ce0B_
not modelled 27.2 31 PDB header:hiv-1 envelope protein
Chain: B: PDB Molecule:protein (leucine zipper model h38-p1);
PDBTitle: trimerization specificity in hiv-1 gp41: analysis with a2 gcn4 leucine zipper model
53c2pqaB_
not modelled 26.5 29 PDB header:replication
Chain: B: PDB Molecule:replication protein a 14 kda subunit;
PDBTitle: crystal structure of full-length human rpa 14/32 heterodimer
54c3ushB_
not modelled 26.5 23 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the q2s0r5 protein from salinibacter ruber,2 northeast structural genomics consortium target srr207
55d1k32a3
not modelled 24.8 10 Fold:7-bladed beta-propeller
Superfamily:Tricorn protease domain 2
Family:Tricorn protease domain 2
56d1iwpa_
not modelled 24.5 16 Fold:TIM beta/alpha-barrel
Superfamily:Cobalamin (vitamin B12)-dependent enzymes
Family:Diol dehydratase, alpha subunit
57d1a06a_
not modelled 23.9 30 Fold:Protein kinase-like (PK-like)
Superfamily:Protein kinase-like (PK-like)
Family:Protein kinases, catalytic subunit
58c2p9mD_
not modelled 23.7 15 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:hypothetical protein mj0922;
PDBTitle: crystal structure of conserved hypothetical protein mj0922 from2 methanocaldococcus jannaschii dsm 2661
59d2pi2e1
not modelled 23.0 29 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
60c3so4C_
not modelled 22.3 18 PDB header:transferase
Chain: C: PDB Molecule:methionine-adenosyltransferase;
PDBTitle: methionine-adenosyltransferase from entamoeba histolytica
61c2zezC_
not modelled 21.9 41 PDB header:hydrolase
Chain: C: PDB Molecule:s-layer associated multidomain endoglucanase;
PDBTitle: family 16 carbohydrate binding module-2
62c3ocmB_
not modelled 21.0 8 PDB header:membrane protein
Chain: B: PDB Molecule:putative membrane protein;
PDBTitle: the crystal structure of a domain from a possible membrane protein of2 bordetella parapertussis
63c1ztaA_
not modelled 20.6 34 PDB header:dna-binding motif
Chain: A: PDB Molecule:leucine zipper monomer;
PDBTitle: the solution structure of a leucine-zipper motif peptide
64c3ol2B_
not modelled 20.4 18 PDB header:signaling protein
Chain: B: PDB Molecule:plexin-b1;
PDBTitle: receptor-ligand structure of human semaphorin 4d with plexin b1.
65d1mlda2
not modelled 19.4 18 Fold:LDH C-terminal domain-like
Superfamily:LDH C-terminal domain-like
Family:Lactate & malate dehydrogenases, C-terminal domain
66c3izcR_
not modelled 18.9 8 PDB header:ribosome
Chain: R: PDB Molecule:60s ribosomal protein rpl18 (l18e);
PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
67c2dfdD_
not modelled 18.4 21 PDB header:oxidoreductase
Chain: D: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of human malate dehydrogenase type 2
68d2f2ac1
not modelled 18.1 16 Fold:Non-globular all-alpha subunits of globular proteins
Superfamily:Glu-tRNAGln amidotransferase C subunit
Family:Glu-tRNAGln amidotransferase C subunit
69c3e5zA_
not modelled 18.0 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative gluconolactonase;
PDBTitle: x-ray structure of the putative gluconolactonase in protein family2 pf08450. northeast structural genomics consortium target drr130.
70c2hpcF_
not modelled 17.7 17 PDB header:blood clotting
Chain: F: PDB Molecule:fibrinogen, gamma polypeptide;
PDBTitle: crystal structure of fragment d from human fibrinogen complexed with2 gly-pro-arg-pro-amide.
71c1u0iA_
not modelled 17.6 33 PDB header:de novo protein
Chain: A: PDB Molecule:iaal-e3;
PDBTitle: iaal-e3/k3 heterodimer
72c2lmiA_
not modelled 17.5 13 PDB header:rna binding protein
Chain: A: PDB Molecule:g-rich sequence factor 1;
PDBTitle: nmr structure of the protein bc040485 from homo sapiens
73c2xzrA_
not modelled 17.1 17 PDB header:cell adhesion
Chain: A: PDB Molecule:immunoglobulin-binding protein eibd;
PDBTitle: escherichia coli immunoglobulin-binding protein eibd 391-438 fused2 to gcn4 adaptors
74c3czoD_
not modelled 17.0 24 PDB header:lyase
Chain: D: PDB Molecule:histidine ammonia-lyase;
PDBTitle: crystal structure of double mutant phenylalanine ammonia-2 lyase from anabaena variabilis
75c2a5wC_
not modelled 16.6 19 PDB header:oxidoreductase
Chain: C: PDB Molecule:sulfite reductase, desulfoviridin-type subunit gamma
PDBTitle: crystal structure of the oxidized gamma-subunit of the dissimilatory2 sulfite reductase (dsrc) from archaeoglobus fulgidus
76c3kpbA_
not modelled 16.5 17 PDB header:unknown function
Chain: A: PDB Molecule:uncharacterized protein mj0100;
PDBTitle: crystal structure of the cbs domain pair of protein mj01002 in complex with 5 -methylthioadenosine and s-adenosyl-l-3 methionine.
77c1mldA_
not modelled 16.4 18 PDB header:oxidoreductase(nad(a)-choh(d))
Chain: A: PDB Molecule:malate dehydrogenase;
PDBTitle: refined structure of mitochondrial malate dehydrogenase2 from porcine heart and the consensus structure for3 dicarboxylic acid oxidoreductases
78c2jjmH_
not modelled 16.1 22 PDB header:transferase
Chain: H: PDB Molecule:glycosyl transferase, group 1 family protein;
PDBTitle: crystal structure of a family gt4 glycosyltransferase from2 bacillus anthracis orf ba1558.
79c2pwzG_
not modelled 15.8 18 PDB header:oxidoreductase
Chain: G: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of the apo form of e.coli malate dehydrogenase
80c2pfiA_
not modelled 15.7 12 PDB header:transport protein
Chain: A: PDB Molecule:chloride channel protein clc-ka;
PDBTitle: crystal structure of the cytoplasmic domain of the human2 chloride channel clc-ka
81d1y5ha3
not modelled 15.6 3 Fold:CBS-domain pair
Superfamily:CBS-domain pair
Family:CBS-domain pair
82c2oszA_
not modelled 15.4 22 PDB header:structural protein
Chain: A: PDB Molecule:nucleoporin p58/p45;
PDBTitle: structure of nup58/45 suggests flexible nuclear pore diameter by2 intermolecular sliding
83c1yx3A_
not modelled 15.2 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein dsrc;
PDBTitle: nmr structure of allochromatium vinosum dsrc: northeast2 structural genomics consortium target op4
84c2v8kA_
not modelled 15.0 35 PDB header:lyase
Chain: A: PDB Molecule:pectate lyase;
PDBTitle: structure of a family 2 pectate lyase in complex with2 trigalacturonic acid
85c2r60A_
not modelled 14.8 24 PDB header:transferase
Chain: A: PDB Molecule:glycosyl transferase, group 1;
PDBTitle: structure of apo sucrose phosphate synthase (sps) of2 halothermothrix orenii
86c3ltjA_
not modelled 14.6 21 PDB header:protein binding
Chain: A: PDB Molecule:alpharep-4;
PDBTitle: structure of a new family of artificial alpha helicoidal repeat2 proteins (alpha-rep) based on thermostable heat-like repeats
87c3m9bK_
not modelled 14.5 20 PDB header:chaperone
Chain: K: PDB Molecule:proteasome-associated atpase;
PDBTitle: crystal structure of the amino terminal coiled coil domain and the2 inter domain of the mycobacterium tuberculosis proteasomal atpase mpa
88c3somO_
not modelled 14.5 23 PDB header:oxidoreductase
Chain: O: PDB Molecule:methylmalonic aciduria and homocystinuria type c protein;
PDBTitle: crystal structure of human mmachc
89c3ue3A_
not modelled 14.3 23 PDB header:transferase
Chain: A: PDB Molecule:septum formation, penicillin binding protein 3,
PDBTitle: crystal structure of acinetobacter baumanni pbp3
90c3idwA_
not modelled 13.9 20 PDB header:endocytosis
Chain: A: PDB Molecule:actin cytoskeleton-regulatory complex protein sla1;
PDBTitle: crystal structure of sla1 homology domain 2
91c3l31B_
not modelled 13.8 10 PDB header:hydrolase
Chain: B: PDB Molecule:probable manganase-dependent inorganic
PDBTitle: crystal structure of the cbs and drtgg domains of the2 regulatory region of clostridium perfringens3 pyrophosphatase complexed with the inhibitor, amp
92c2d4zB_
not modelled 13.8 21 PDB header:transport protein
Chain: B: PDB Molecule:chloride channel protein;
PDBTitle: crystal structure of the cytoplasmic domain of the chloride channel2 clc-0
93c2qh1B_
not modelled 13.7 18 PDB header:unknown function
Chain: B: PDB Molecule:hypothetical protein ta0289;
PDBTitle: structure of ta289, a cbs-rubredoxin-like protein, in its fe+2-bound2 state
94d1rp3a2
not modelled 13.4 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
95d1o50a3
not modelled 13.2 15 Fold:CBS-domain pair
Superfamily:CBS-domain pair
Family:CBS-domain pair
96d1wi9a_
not modelled 12.9 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PCI domain (PINT motif)
97c3kfuJ_
not modelled 12.9 26 PDB header:ligase/rna
Chain: J: PDB Molecule:glutamyl-trna(gln) amidotransferase subunit c;
PDBTitle: crystal structure of the transamidosome
98d1n0ua3
not modelled 12.8 26 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Translational machinery components
99d2ca1a1
not modelled 12.7 21 Fold:Nucleocapsid protein dimerization domain
Superfamily:Nucleocapsid protein dimerization domain
Family:Coronavirus nucleocapsid protein

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