Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A6J8
DateThu Jan 5 11:03:18 GMT 2012
Unique Job ID977e49d2e5c4a942

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3i12A_
Top template information
PDB header:ligase
Chain: A: PDB Molecule:d-alanine-d-alanine ligase a;
PDBTitle: the crystal structure of the d-alanyl-alanine synthetase a from2 salmonella enterica subsp. enterica serovar typhimurium str. lt2
Confidence and coverage
Confidence:100.0% Coverage: 99%
360 residues ( 99% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MEKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKSRFDVVLLGIDKQGQWHVSDASNYLLN
Secondary structure 
SS confidence 
Disorder  ????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ADDPAHIALRPSATSLAQVPGKHEHQLIDAQNGQPLPTVDVIFPIVHGTLGEDGSLQGML
Secondary structure 
SS confidence 
Disorder 
?
??
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  RVANLPFVGSDVLASAACMDKDVTKRLLRDAGLNIAPFITLTRANRHNISFAEVESKLGL
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  PLFVKPANQGSSVGVSKVTSEEQYAIAVDLAFEFDHKVIVEQGIKGREIECAVLGNDNPQ
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  ASTCGEIVLTSDFYAYDTKYIDEDGAKVVVPAAIAPEINDKIRAIAVQAYQTLGCAGMAR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  VDVFLTPENEVVINEINTLPGFTNISMYPKLWQASGLGYTDLITRLIELALERHAADNAL
Secondary structure 
SS confidence 
Disorder 
??
???
Disorder confidence 
 
   ....
Sequence  KTTM
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 3i12 chain A

3D model

Region: 2 - 363
Aligned: 360
Modelled: 362
Confidence: 100.0%
Identity: 90%
PDB header:ligase
Chain: A: PDB Molecule:d-alanine-d-alanine ligase a;
PDBTitle: the crystal structure of the d-alanyl-alanine synthetase a from2 salmonella enterica subsp. enterica serovar typhimurium str. lt2

Phyre2

PDB 1ehi chain B

3D model

Region: 2 - 364
Aligned: 340
Modelled: 346
Confidence: 100.0%
Identity: 36%
PDB header:ligase
Chain: B: PDB Molecule:d-alanine:d-lactate ligase;
PDBTitle: d-alanine:d-lactate ligase (lmddl2) of vancomycin-resistant2 leuconostoc mesenteroides

Phyre2

PDB 3e5n chain A

3D model

Region: 2 - 360
Aligned: 340
Modelled: 342
Confidence: 100.0%
Identity: 64%
PDB header:ligase
Chain: A: PDB Molecule:d-alanine-d-alanine ligase a;
PDBTitle: crystal strucutre of d-alanine-d-alanine ligase from2 xanthomonas oryzae pv. oryzae kacc10331

Phyre2

PDB 2i80 chain B

3D model

Region: 3 - 363
Aligned: 338
Modelled: 350
Confidence: 100.0%
Identity: 41%
PDB header:ligase
Chain: B: PDB Molecule:d-alanine-d-alanine ligase;
PDBTitle: allosteric inhibition of staphylococcus aureus d-alanine:d-alanine2 ligase revealed by crystallographic studies

Phyre2

PDB 3tqt chain B

3D model

Region: 3 - 363
Aligned: 332
Modelled: 339
Confidence: 100.0%
Identity: 41%
PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: structure of the d-alanine-d-alanine ligase from coxiella burnetii

Phyre2

PDB 1e4e chain B

3D model

Region: 2 - 351
Aligned: 336
Modelled: 350
Confidence: 100.0%
Identity: 37%
PDB header:ligase
Chain: B: PDB Molecule:vancomycin/teicoplanin a-type resistance protein vana;
PDBTitle: d-alanyl-d-lacate ligase

Phyre2

PDB 3se7 chain A

3D model

Region: 2 - 351
Aligned: 326
Modelled: 340
Confidence: 100.0%
Identity: 39%
PDB header:ligase
Chain: A: PDB Molecule:vana;
PDBTitle: ancient vana

Phyre2

PDB 3k3p chain A

3D model

Region: 3 - 357
Aligned: 314
Modelled: 322
Confidence: 100.0%
Identity: 38%
PDB header:ligase
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of the apo form of d-alanine:d-alanine ligase (ddl)2 from streptococcus mutans

Phyre2

PDB 2dln chain A

3D model

Region: 1 - 350
Aligned: 302
Modelled: 307
Confidence: 100.0%
Identity: 36%
PDB header:ligase(peptidoglycan synthesis)
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: vancomycin resistance: structure of d-alanine:d-alanine2 ligase at 2.3 angstroms resolution

Phyre2

PDB 3lwb chain A

3D model

Region: 2 - 353
Aligned: 314
Modelled: 322
Confidence: 100.0%
Identity: 45%
PDB header:ligase
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of apo d-alanine:d-alanine ligase (ddl) from2 mycobacterium tuberculosis

Phyre2

PDB 2zdq chain A

3D model

Region: 4 - 351
Aligned: 317
Modelled: 326
Confidence: 100.0%
Identity: 41%
PDB header:ligase
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of d-alanine:d-alanine ligase with atp2 and d-alanine:d-alanine from thermus thermophius hb8

Phyre2

PDB 2pvp chain B

3D model

Region: 3 - 346
Aligned: 310
Modelled: 326
Confidence: 100.0%
Identity: 26%
PDB header:ligase
Chain: B: PDB Molecule:d-alanine-d-alanine ligase;
PDBTitle: crystal structure of d-alanine-d-alanine ligase from helicobacter2 pylori

Phyre2

PDB 3r23 chain B

3D model

Region: 4 - 357
Aligned: 298
Modelled: 310
Confidence: 100.0%
Identity: 31%
PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of d-alanine--d-alanine ligase from bacillus2 anthracis

Phyre2

PDB 1m6v chain E

3D model

Region: 1 - 346
Aligned: 307
Modelled: 331
Confidence: 100.0%
Identity: 17%
PDB header:ligase
Chain: E: PDB Molecule:carbamoyl phosphate synthetase large chain;
PDBTitle: crystal structure of the g359f (small subunit) point mutant of2 carbamoyl phosphate synthetase

Phyre2

PDB 3ouz chain A

3D model

Region: 1 - 351
Aligned: 306
Modelled: 324
Confidence: 100.0%
Identity: 19%
PDB header:ligase
Chain: A: PDB Molecule:biotin carboxylase;
PDBTitle: crystal structure of biotin carboxylase-adp complex from campylobacter2 jejuni

Phyre2

PDB 3bg5 chain C

3D model

Region: 1 - 351
Aligned: 305
Modelled: 325
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: C: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase

Phyre2

PDB 2dzd chain B

3D model

Region: 1 - 347
Aligned: 304
Modelled: 322
Confidence: 100.0%
Identity: 17%
PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of the biotin carboxylase domain of2 pyruvate carboxylase

Phyre2

PDB 1ulz chain A

3D model

Region: 1 - 351
Aligned: 305
Modelled: 327
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:pyruvate carboxylase n-terminal domain;
PDBTitle: crystal structure of the biotin carboxylase subunit of pyruvate2 carboxylase

Phyre2

PDB 3g8c chain B

3D model

Region: 1 - 347
Aligned: 308
Modelled: 324
Confidence: 100.0%
Identity: 17%
PDB header:ligase
Chain: B: PDB Molecule:biotin carboxylase;
PDBTitle: crystal stucture of biotin carboxylase in complex with2 biotin, bicarbonate, adp and mg ion

Phyre2

PDB 1kjj chain A

3D model

Region: 4 - 347
Aligned: 288
Modelled: 312
Confidence: 100.0%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s

Phyre2
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c3i12A_
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c1ehiB_
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c3e5nA_
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c2i80B_
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c3tqtB_
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c1e4eB_
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c3se7A_
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c3k3pA_
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c2dlnA_
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c3lwbA_
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c2zdqA_
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c2pvpB_
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c3r23B_
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c1m6vE_
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c3ouzA_
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c3bg5C_
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c2dzdB_
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c1ulzA_
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c3g8cB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3i12A_
100.0 90 PDB header:ligase
Chain: A: PDB Molecule:d-alanine-d-alanine ligase a;
PDBTitle: the crystal structure of the d-alanyl-alanine synthetase a from2 salmonella enterica subsp. enterica serovar typhimurium str. lt2
2c1ehiB_
100.0 36 PDB header:ligase
Chain: B: PDB Molecule:d-alanine:d-lactate ligase;
PDBTitle: d-alanine:d-lactate ligase (lmddl2) of vancomycin-resistant2 leuconostoc mesenteroides
3c3e5nA_
100.0 64 PDB header:ligase
Chain: A: PDB Molecule:d-alanine-d-alanine ligase a;
PDBTitle: crystal strucutre of d-alanine-d-alanine ligase from2 xanthomonas oryzae pv. oryzae kacc10331
4c2i80B_
100.0 41 PDB header:ligase
Chain: B: PDB Molecule:d-alanine-d-alanine ligase;
PDBTitle: allosteric inhibition of staphylococcus aureus d-alanine:d-alanine2 ligase revealed by crystallographic studies
5c3tqtB_
100.0 41 PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: structure of the d-alanine-d-alanine ligase from coxiella burnetii
6c1e4eB_
100.0 37 PDB header:ligase
Chain: B: PDB Molecule:vancomycin/teicoplanin a-type resistance protein vana;
PDBTitle: d-alanyl-d-lacate ligase
7c3se7A_
100.0 39 PDB header:ligase
Chain: A: PDB Molecule:vana;
PDBTitle: ancient vana
8c3k3pA_
100.0 38 PDB header:ligase
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of the apo form of d-alanine:d-alanine ligase (ddl)2 from streptococcus mutans
9c2dlnA_
100.0 36 PDB header:ligase(peptidoglycan synthesis)
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: vancomycin resistance: structure of d-alanine:d-alanine2 ligase at 2.3 angstroms resolution
10c3lwbA_
100.0 45 PDB header:ligase
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of apo d-alanine:d-alanine ligase (ddl) from2 mycobacterium tuberculosis
11c2zdqA_
100.0 41 PDB header:ligase
Chain: A: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of d-alanine:d-alanine ligase with atp2 and d-alanine:d-alanine from thermus thermophius hb8
12c2pvpB_
100.0 26 PDB header:ligase
Chain: B: PDB Molecule:d-alanine-d-alanine ligase;
PDBTitle: crystal structure of d-alanine-d-alanine ligase from helicobacter2 pylori
13c3r23B_
100.0 31 PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of d-alanine--d-alanine ligase from bacillus2 anthracis
14c1m6vE_
100.0 17 PDB header:ligase
Chain: E: PDB Molecule:carbamoyl phosphate synthetase large chain;
PDBTitle: crystal structure of the g359f (small subunit) point mutant of2 carbamoyl phosphate synthetase
15c3ouzA_
100.0 19 PDB header:ligase
Chain: A: PDB Molecule:biotin carboxylase;
PDBTitle: crystal structure of biotin carboxylase-adp complex from campylobacter2 jejuni
16c3bg5C_
100.0 18 PDB header:ligase
Chain: C: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase
17c2dzdB_
100.0 17 PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of the biotin carboxylase domain of2 pyruvate carboxylase
18c1ulzA_
100.0 18 PDB header:ligase
Chain: A: PDB Molecule:pyruvate carboxylase n-terminal domain;
PDBTitle: crystal structure of the biotin carboxylase subunit of pyruvate2 carboxylase
19c3g8cB_
100.0 17 PDB header:ligase
Chain: B: PDB Molecule:biotin carboxylase;
PDBTitle: crystal stucture of biotin carboxylase in complex with2 biotin, bicarbonate, adp and mg ion
20c1kjjA_
100.0 20 PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s
21c2vpqA_
not modelled 100.0 17 PDB header:ligase
Chain: A: PDB Molecule:acetyl-coa carboxylase;
PDBTitle: crystal structure of biotin carboxylase from s. aureus2 complexed with amppnp
22c1w96B_
not modelled 100.0 15 PDB header:ligase
Chain: B: PDB Molecule:acetyl-coenzyme a carboxylase;
PDBTitle: crystal structure of biotin carboxylase domain of acetyl-2 coenzyme a carboxylase from saccharomyces cerevisiae in3 complex with soraphen a
23c3q2oB_
not modelled 100.0 19 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase
24c2hjwA_
not modelled 100.0 15 PDB header:ligase
Chain: A: PDB Molecule:acetyl-coa carboxylase 2;
PDBTitle: crystal structure of the bc domain of acc2
25c3u9sE_
not modelled 100.0 19 PDB header:ligase
Chain: E: PDB Molecule:methylcrotonyl-coa carboxylase, alpha-subunit;
PDBTitle: crystal structure of p. aeruginosa 3-methylcrotonyl-coa carboxylase2 (mcc) 750 kd holoenzyme, coa complex
26c3n6rK_
not modelled 100.0 17 PDB header:ligase
Chain: K: PDB Molecule:propionyl-coa carboxylase, alpha subunit;
PDBTitle: crystal structure of the holoenzyme of propionyl-coa carboxylase (pcc)
27c2xd4A_
not modelled 100.0 17 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: nucleotide-bound structures of bacillus subtilis glycinamide2 ribonucleotide synthetase
28c3gidB_
not modelled 100.0 13 PDB header:ligase
Chain: B: PDB Molecule:acetyl-coa carboxylase 2;
PDBTitle: the biotin carboxylase (bc) domain of human acetyl-coa2 carboxylase 2 (acc2) in complex with soraphen a
29c2gpwC_
not modelled 100.0 17 PDB header:ligase
Chain: C: PDB Molecule:biotin carboxylase;
PDBTitle: crystal structure of the biotin carboxylase subunit, f363a2 mutant, of acetyl-coa carboxylase from escherichia coli.
30c3lp8A_
not modelled 100.0 17 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine-glycine ligase;
PDBTitle: crystal structure of phosphoribosylamine-glycine ligase from2 ehrlichia chaffeensis
31d1ehia2
not modelled 100.0 37 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
32c2yyaB_
not modelled 100.0 16 PDB header:ligase
Chain: B: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of gar synthetase from aquifex aeolicus
33c3uvzB_
not modelled 100.0 17 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase, atpase2 subunit from burkholderia ambifaria
34c1vkzA_
not modelled 100.0 16 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of phosphoribosylamine--glycine ligase (tm1250) from2 thermotoga maritima at 2.30 a resolution
35c3etjB_
not modelled 100.0 20 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase atpase
PDBTitle: crystal structure e. coli purk in complex with mg, adp, and2 pi
36c3orqA_
not modelled 100.0 20 PDB header:ligase,biosynthetic protein
Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide synthetase;
PDBTitle: crystal structure of n5-carboxyaminoimidazole synthetase from2 staphylococcus aureus complexed with adp
37c3k5iB_
not modelled 100.0 21 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosyl-aminoimidazole carboxylase;
PDBTitle: crystal structure of n5-carboxyaminoimidazole synthase from2 aspergillus clavatus in complex with adp and 5-3 aminoimadazole ribonucleotide
38c2ip4A_
not modelled 100.0 15 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of glycinamide ribonucleotide synthetase from2 thermus thermophilus hb8
39c2qk4A_
not modelled 100.0 17 PDB header:ligase
Chain: A: PDB Molecule:trifunctional purine biosynthetic protein adenosine-3;
PDBTitle: human glycinamide ribonucleotide synthetase
40c2ys6A_
not modelled 100.0 15 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylglycinamide synthetase;
PDBTitle: crystal structure of gar synthetase from geobacillus kaustophilus
41c2dwcB_
not modelled 100.0 20 PDB header:transferase
Chain: B: PDB Molecule:433aa long hypothetical phosphoribosylglycinamide formyl
PDBTitle: crystal structure of probable phosphoribosylglycinamide formyl2 transferase from pyrococcus horikoshii ot3 complexed with adp
42c1gsoA_
not modelled 100.0 15 PDB header:ligase
Chain: A: PDB Molecule:protein (glycinamide ribonucleotide synthetase);
PDBTitle: glycinamide ribonucleotide synthetase (gar-syn) from e.2 coli.
43d1e4ea2
not modelled 100.0 37 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
44d1iowa2
not modelled 100.0 34 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
45c2pn1A_
not modelled 100.0 18 PDB header:ligase
Chain: A: PDB Molecule:carbamoylphosphate synthase large subunit;
PDBTitle: crystal structure of carbamoylphosphate synthase large subunit (split2 gene in mj) (zp_00538348.1) from exiguobacterium sp. 255-15 at 2.00 a3 resolution
46c2r85B_
not modelled 100.0 17 PDB header:unknown function
Chain: B: PDB Molecule:purp protein pf1517;
PDBTitle: crystal structure of purp from pyrococcus furiosus complexed with amp
47c3df7A_
not modelled 100.0 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative atp-grasp superfamily protein;
PDBTitle: crystal structure of a putative atp-grasp superfamily2 protein from archaeoglobus fulgidus
48c2z04A_
not modelled 100.0 20 PDB header:lyase
Chain: A: PDB Molecule:phosphoribosylaminoimidazole carboxylase atpase
PDBTitle: crystal structure of phosphoribosylaminoimidazole2 carboxylase atpase subunit from aquifex aeolicus
49c1uc8B_
not modelled 100.0 17 PDB header:biosynthetic protein
Chain: B: PDB Molecule:lysine biosynthesis enzyme;
PDBTitle: crystal structure of a lysine biosynthesis enzyme, lysx,2 from thermus thermophilus hb8
50c1z2pX_
not modelled 100.0 11 PDB header:transferase
Chain: X: PDB Molecule:inositol 1,3,4-trisphosphate 5/6-kinase;
PDBTitle: inositol 1,3,4-trisphosphate 5/6-kinase in complex with mg2+/amp-2 pcp/ins(1,3,4)p3
51d1w96a3
not modelled 100.0 15 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
52d2r7ka2
not modelled 100.0 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
53d1a9xa5
not modelled 100.0 14 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
54d2r85a2
not modelled 99.9 16 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
55c3ln6A_
not modelled 99.9 21 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 streptococcus agalactiae
56c1i7nA_
not modelled 99.9 13 PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin ii;
PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain
57d1vkza3
not modelled 99.9 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
58c2qb5B_
not modelled 99.9 20 PDB header:transferase
Chain: B: PDB Molecule:inositol-tetrakisphosphate 1-kinase;
PDBTitle: crystal structure of human inositol 1,3,4-trisphosphate 5/6-kinase2 (itpk1) in complex with adp and mn2+
59c2p0aA_
not modelled 99.9 14 PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin-3;
PDBTitle: the crystal structure of human synapsin iii (syn3) in complex with2 amppnp
60d3etja3
not modelled 99.9 20 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
61c1pk8D_
not modelled 99.9 12 PDB header:membrane protein
Chain: D: PDB Molecule:rat synapsin i;
PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp
62d1kjqa3
not modelled 99.9 21 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
63d2j9ga3
not modelled 99.9 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
64d1ulza3
not modelled 99.9 16 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
65d1a9xa6
not modelled 99.9 18 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
66c2qf7A_
not modelled 99.9 18 PDB header:ligase
Chain: A: PDB Molecule:pyruvate carboxylase protein;
PDBTitle: crystal structure of a complete multifunctional pyruvate carboxylase2 from rhizobium etli
67c3ln7A_
not modelled 99.9 22 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 pasteurella multocida
68d1gsoa3
not modelled 99.9 12 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
69d1uc8a2
not modelled 99.9 16 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Lysine biosynthesis enzyme LysX ATP-binding domain
70c1gshA_
not modelled 99.9 12 PDB header:glutathione biosynthesis ligase
Chain: A: PDB Molecule:glutathione biosynthetic ligase;
PDBTitle: structure of escherichia coli glutathione synthetase at ph 7.5
71d1pk8a2
not modelled 99.9 12 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Synapsin C-terminal domain
72c3t9aA_
not modelled 99.9 15 PDB header:transferase
Chain: A: PDB Molecule:inositol pyrophosphate kinase;
PDBTitle: crystal structure of the catalytic domain of human diphosphoinositol2 pentakisphosphate kinase 2 (ppip5k2) in complex with amppnp at ph 7.0
73d1i7na2
not modelled 99.9 13 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Synapsin C-terminal domain
74d1e4ea1
not modelled 99.8 36 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:D-Alanine ligase N-terminal domain
75d1ehia1
not modelled 99.8 32 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:D-Alanine ligase N-terminal domain
76d1iowa1
not modelled 99.7 36 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:D-Alanine ligase N-terminal domain
77c2r7mA_
not modelled 99.6 16 PDB header:ligase
Chain: A: PDB Molecule:5-formaminoimidazole-4-carboxamide-1-(beta)-d-
PDBTitle: crystal structure of faicar synthetase (purp) from m.2 jannaschii complexed with amp
78d1gsaa2
not modelled 99.5 12 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
79c2cqyA_
not modelled 99.1 22 PDB header:ligase
Chain: A: PDB Molecule:propionyl-coa carboxylase alpha chain,
PDBTitle: solution structure of b domain from human propionyl-coa2 carboxylase alpha subunit
80c2pbzC_
not modelled 99.1 18 PDB header:ligase
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of an imp biosynthesis protein purp from2 thermococcus kodakaraensis
81d1a9xa4
not modelled 99.0 18 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
82c1wr2A_
not modelled 98.7 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ph1789;
PDBTitle: crystal structure of ph1788 from pyrococcus horikoshii ot3
83c2nu9E_
not modelled 98.7 18 PDB header:ligase
Chain: E: PDB Molecule:succinyl-coa synthetase beta chain;
PDBTitle: c123at mutant of e. coli succinyl-coa synthetase2 orthorhombic crystal form
84d1eucb2
not modelled 98.6 18 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Succinyl-CoA synthetase, beta-chain, N-terminal domain
85d1a9xa3
not modelled 98.6 15 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
86c1eucB_
not modelled 98.6 18 PDB header:ligase
Chain: B: PDB Molecule:succinyl-coa synthetase, beta chain;
PDBTitle: crystal structure of dephosphorylated pig heart, gtp-2 specific succinyl-coa synthetase
87d2nu7b2
not modelled 98.5 16 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Succinyl-CoA synthetase, beta-chain, N-terminal domain
88d2pbza2
not modelled 98.5 19 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
89c3tinA_
not modelled 98.5 15 PDB header:ligase
Chain: A: PDB Molecule:ttl protein;
PDBTitle: tubulin tyrosine ligase
90d1kjqa2
not modelled 98.4 19 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
91d1ulza2
not modelled 98.1 16 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
92d2j9ga2
not modelled 98.0 13 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
93c3mwdA_
not modelled 97.2 14 PDB header:transferase
Chain: A: PDB Molecule:atp-citrate synthase;
PDBTitle: truncated human atp-citrate lyase with citrate bound
94d1w96a2
not modelled 97.0 15 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
95d2jfga1
not modelled 96.8 12 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
96c2xdoC_
not modelled 96.3 17 PDB header:oxidoreductase
Chain: C: PDB Molecule:tetx2 protein;
PDBTitle: structure of the tetracycline degrading monooxygenase tetx2 from2 bacteroides thetaiotaomicron
97d1gsoa2
not modelled 96.0 16 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
98c3i3lA_
not modelled 95.9 21 PDB header:hydrolase
Chain: A: PDB Molecule:alkylhalidase cmls;
PDBTitle: crystal structure of cmls, a flavin-dependent halogenase
99c3kljA_
not modelled 95.4 9 PDB header:oxidoreductase
Chain: A: PDB Molecule:nad(fad)-dependent dehydrogenase, nirb-family (n-terminal
PDBTitle: crystal structure of nadh:rubredoxin oxidoreductase from clostridium2 acetobutylicum
100c1ps9A_
not modelled 95.4 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:2,4-dienoyl-coa reductase;
PDBTitle: the crystal structure and reaction mechanism of e. coli 2,4-2 dienoyl coa reductase
101d1e5qa1
not modelled 94.8 14 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
102c3ic5A_
not modelled 94.7 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative saccharopine dehydrogenase;
PDBTitle: n-terminal domain of putative saccharopine dehydrogenase from ruegeria2 pomeroyi.
103c2hkoA_
not modelled 94.4 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:lysine-specific histone demethylase 1;
PDBTitle: crystal structure of lsd1
104c1djnB_
not modelled 94.3 25 PDB header:oxidoreductase
Chain: B: PDB Molecule:trimethylamine dehydrogenase;
PDBTitle: structural and biochemical characterization of recombinant wild type2 trimethylamine dehydrogenase from methylophilus methylotrophus (sp.3 w3a1)
105c3k30B_
not modelled 94.3 26 PDB header:oxidoreductase
Chain: B: PDB Molecule:histamine dehydrogenase;
PDBTitle: histamine dehydrogenase from nocardiodes simplex
106d1ps9a3
not modelled 94.3 13 Fold:Nucleotide-binding domain
Superfamily:Nucleotide-binding domain
Family:N-terminal domain of adrenodoxin reductase-like
107c2e1mA_
not modelled 94.3 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-glutamate oxidase;
PDBTitle: crystal structure of l-glutamate oxidase from streptomyces sp. x-119-6
108c1e5lA_
not modelled 94.2 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:saccharopine reductase;
PDBTitle: apo saccharopine reductase from magnaporthe grisea
109c3rhaA_
not modelled 94.2 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:putrescine oxidase;
PDBTitle: the crystal structure of oxidoreductase from arthrobacter aurescens
110c3atrA_
not modelled 94.1 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:conserved archaeal protein;
PDBTitle: geranylgeranyl reductase (ggr) from sulfolobus acidocaldarius co-2 crystallized with its ligand
111c2xagA_
not modelled 94.0 20 PDB header:transcription
Chain: A: PDB Molecule:lysine-specific histone demethylase 1;
PDBTitle: crystal structure of lsd1-corest in complex with para-bromo-2 (-)-trans-2-phenylcyclopropyl-1-amine
112c2v1dA_
not modelled 94.0 20 PDB header:oxidoreductase/repressor
Chain: A: PDB Molecule:lysine-specific histone demethylase 1;
PDBTitle: structural basis of lsd1-corest selectivity in histone h32 recognition
113c3allA_
not modelled 94.0 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase;
PDBTitle: crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid2 oxygenase, mutant y270a
114c2vdcI_
not modelled 94.0 13 PDB header:oxidoreductase
Chain: I: PDB Molecule:glutamate synthase [nadph] small chain;
PDBTitle: the 9.5 a resolution structure of glutamate synthase from2 cryo-electron microscopy and its oligomerization behavior3 in solution: functional implications.
115c2eq8E_
not modelled 94.0 8 PDB header:oxidoreductase
Chain: E: PDB Molecule:pyruvate dehydrogenase complex, dihydrolipoamide
PDBTitle: crystal structure of lipoamide dehydrogenase from thermus thermophilus2 hb8 with psbdp
116c1vdcA_
not modelled 93.9 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadph dependent thioredoxin reductase;
PDBTitle: structure of nadph dependent thioredoxin reductase
117d1djqa3
not modelled 93.9 25 Fold:Nucleotide-binding domain
Superfamily:Nucleotide-binding domain
Family:N-terminal domain of adrenodoxin reductase-like
118c1c0iA_
not modelled 93.9 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-amino acid oxidase;
PDBTitle: crystal structure of d-amino acid oxidase in complex with2 two anthranylate molecules
119d2dw4a2
not modelled 93.9 22 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD-linked reductases, N-terminal domain
120c1f8sA_
not modelled 93.9 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-amino acid oxidase;
PDBTitle: crystal structure of l-amino acid oxidase from calloselasma2 rhodostoma, complexed with three molecules of o-aminobenzoate.

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