Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP07862
DateThu Jan 5 11:00:37 GMT 2012
Unique Job IDd8c50704caed0015

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2dlnA_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage:100%
306 residues (100% 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  MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFI
Secondary structure 
SS confidence 
Disorder  ???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  EFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIE
Secondary structure 
SS confidence 
Disorder  ????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  KWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQAL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  VLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   ......
Sequence  ILELAD
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 2dln chain A

3D model

Region: 1 - 306
Aligned: 306
Modelled: 306
Confidence: 100.0%
Identity: 100%
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 2i80 chain B

3D model

Region: 2 - 305
Aligned: 296
Modelled: 304
Confidence: 100.0%
Identity: 35%
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 1ehi chain B

3D model

Region: 2 - 305
Aligned: 288
Modelled: 304
Confidence: 100.0%
Identity: 31%
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 3i12 chain A

3D model

Region: 2 - 305
Aligned: 301
Modelled: 304
Confidence: 100.0%
Identity: 35%
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 1e4e chain B

3D model

Region: 2 - 305
Aligned: 295
Modelled: 304
Confidence: 100.0%
Identity: 34%
PDB header:ligase
Chain: B: PDB Molecule:vancomycin/teicoplanin a-type resistance protein vana;
PDBTitle: d-alanyl-d-lacate ligase

Phyre2

PDB 3tqt chain B

3D model

Region: 2 - 305
Aligned: 284
Modelled: 286
Confidence: 100.0%
Identity: 29%
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 3e5n chain A

3D model

Region: 2 - 305
Aligned: 288
Modelled: 304
Confidence: 100.0%
Identity: 38%
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 3se7 chain A

3D model

Region: 2 - 305
Aligned: 289
Modelled: 298
Confidence: 100.0%
Identity: 36%
PDB header:ligase
Chain: A: PDB Molecule:vana;
PDBTitle: ancient vana

Phyre2

PDB 3r23 chain B

3D model

Region: 3 - 305
Aligned: 291
Modelled: 302
Confidence: 100.0%
Identity: 34%
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 3lwb chain A

3D model

Region: 2 - 305
Aligned: 293
Modelled: 304
Confidence: 100.0%
Identity: 34%
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: 3 - 305
Aligned: 292
Modelled: 303
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: 2 - 304
Aligned: 278
Modelled: 289
Confidence: 100.0%
Identity: 29%
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 3k3p chain A

3D model

Region: 2 - 305
Aligned: 279
Modelled: 290
Confidence: 100.0%
Identity: 32%
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 1m6v chain E

3D model

Region: 3 - 301
Aligned: 283
Modelled: 299
Confidence: 100.0%
Identity: 19%
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 1ulz chain A

3D model

Region: 1 - 301
Aligned: 279
Modelled: 296
Confidence: 100.0%
Identity: 21%
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 - 301
Aligned: 279
Modelled: 301
Confidence: 100.0%
Identity: 22%
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 2dzd chain B

3D model

Region: 2 - 301
Aligned: 276
Modelled: 295
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of the biotin carboxylase domain of2 pyruvate carboxylase

Phyre2

PDB 3ouz chain A

3D model

Region: 2 - 301
Aligned: 277
Modelled: 285
Confidence: 100.0%
Identity: 23%
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: 2 - 301
Aligned: 274
Modelled: 300
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: C: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase

Phyre2

PDB 1kjj chain A

3D model

Region: 2 - 302
Aligned: 269
Modelled: 301
Confidence: 100.0%
Identity: 18%
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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c2dlnA_
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c2i80B_
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c1ehiB_
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c3i12A_
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c1e4eB_
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c3tqtB_
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c3e5nA_
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c3se7A_
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c3r23B_
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c3lwbA_
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c2zdqA_
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c2pvpB_
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c3k3pA_
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c1m6vE_
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c1ulzA_
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c3g8cB_
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c2dzdB_
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c3ouzA_
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c3bg5C_
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c1kjjA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2dlnA_
100.0 100 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
2c2i80B_
100.0 35 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
3c1ehiB_
100.0 31 PDB header:ligase
Chain: B: PDB Molecule:d-alanine:d-lactate ligase;
PDBTitle: d-alanine:d-lactate ligase (lmddl2) of vancomycin-resistant2 leuconostoc mesenteroides
4c3i12A_
100.0 35 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
5c1e4eB_
100.0 34 PDB header:ligase
Chain: B: PDB Molecule:vancomycin/teicoplanin a-type resistance protein vana;
PDBTitle: d-alanyl-d-lacate ligase
6c3tqtB_
100.0 29 PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: structure of the d-alanine-d-alanine ligase from coxiella burnetii
7c3e5nA_
100.0 38 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
8c3se7A_
100.0 36 PDB header:ligase
Chain: A: PDB Molecule:vana;
PDBTitle: ancient vana
9c3r23B_
100.0 34 PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of d-alanine--d-alanine ligase from bacillus2 anthracis
10c3lwbA_
100.0 34 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 29 PDB header:ligase
Chain: B: PDB Molecule:d-alanine-d-alanine ligase;
PDBTitle: crystal structure of d-alanine-d-alanine ligase from helicobacter2 pylori
13c3k3pA_
100.0 32 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
14c1m6vE_
100.0 19 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
15c1ulzA_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:pyruvate carboxylase n-terminal domain;
PDBTitle: crystal structure of the biotin carboxylase subunit of pyruvate2 carboxylase
16c3g8cB_
100.0 22 PDB header:ligase
Chain: B: PDB Molecule:biotin carboxylase;
PDBTitle: crystal stucture of biotin carboxylase in complex with2 biotin, bicarbonate, adp and mg ion
17c2dzdB_
100.0 21 PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of the biotin carboxylase domain of2 pyruvate carboxylase
18c3ouzA_
100.0 23 PDB header:ligase
Chain: A: PDB Molecule:biotin carboxylase;
PDBTitle: crystal structure of biotin carboxylase-adp complex from campylobacter2 jejuni
19c3bg5C_
100.0 18 PDB header:ligase
Chain: C: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase
20c1kjjA_
100.0 18 PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s
21c2xd4A_
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
22d1iowa2
not modelled 100.0 100 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
23c2hjwA_
not modelled 100.0 20 PDB header:ligase
Chain: A: PDB Molecule:acetyl-coa carboxylase 2;
PDBTitle: crystal structure of the bc domain of acc2
24c2vpqA_
not modelled 100.0 18 PDB header:ligase
Chain: A: PDB Molecule:acetyl-coa carboxylase;
PDBTitle: crystal structure of biotin carboxylase from s. aureus2 complexed with amppnp
25c2yyaB_
not modelled 100.0 18 PDB header:ligase
Chain: B: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of gar synthetase from aquifex aeolicus
26c1w96B_
not modelled 100.0 19 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
27c3lp8A_
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
28c3gidB_
not modelled 100.0 18 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
29c1vkzA_
not modelled 100.0 15 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
30c2ip4A_
not modelled 100.0 19 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of glycinamide ribonucleotide synthetase from2 thermus thermophilus hb8
31c2qk4A_
not modelled 100.0 17 PDB header:ligase
Chain: A: PDB Molecule:trifunctional purine biosynthetic protein adenosine-3;
PDBTitle: human glycinamide ribonucleotide synthetase
32c3q2oB_
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
33c3n6rK_
not modelled 100.0 19 PDB header:ligase
Chain: K: PDB Molecule:propionyl-coa carboxylase, alpha subunit;
PDBTitle: crystal structure of the holoenzyme of propionyl-coa carboxylase (pcc)
34c2gpwC_
not modelled 100.0 22 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.
35c3u9sE_
not modelled 100.0 23 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
36c3k5iB_
not modelled 100.0 19 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
37c3uvzB_
not modelled 100.0 18 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase, atpase2 subunit from burkholderia ambifaria
38c2ys6A_
not modelled 100.0 19 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylglycinamide synthetase;
PDBTitle: crystal structure of gar synthetase from geobacillus kaustophilus
39c3etjB_
not modelled 100.0 18 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase atpase
PDBTitle: crystal structure e. coli purk in complex with mg, adp, and2 pi
40d1ehia2
not modelled 100.0 26 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
41c3orqA_
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
42d1e4ea2
not modelled 100.0 32 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
43c1gsoA_
not modelled 100.0 16 PDB header:ligase
Chain: A: PDB Molecule:protein (glycinamide ribonucleotide synthetase);
PDBTitle: glycinamide ribonucleotide synthetase (gar-syn) from e.2 coli.
44c2dwcB_
not modelled 100.0 17 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
45c3df7A_
not modelled 100.0 16 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
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
47c2pn1A_
not modelled 100.0 20 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
48c1uc8B_
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
49c1z2pX_
not modelled 100.0 13 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
50c2z04A_
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
51d1w96a3
not modelled 100.0 20 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
52c3ln6A_
not modelled 100.0 17 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 streptococcus agalactiae
53d1a9xa5
not modelled 100.0 16 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
54c1i7nA_
not modelled 100.0 16 PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin ii;
PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain
55d1vkza3
not modelled 100.0 14 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
56c1pk8D_
not modelled 100.0 16 PDB header:membrane protein
Chain: D: PDB Molecule:rat synapsin i;
PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp
57d2r7ka2
not modelled 100.0 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
58c2qb5B_
not modelled 100.0 14 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 100.0 16 PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin-3;
PDBTitle: the crystal structure of human synapsin iii (syn3) in complex with2 amppnp
60d2r85a2
not modelled 99.9 15 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
61d2j9ga3
not modelled 99.9 20 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
62d1ulza3
not modelled 99.9 20 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
63d3etja3
not modelled 99.9 21 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
64d1a9xa6
not modelled 99.9 18 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
65c3ln7A_
not modelled 99.9 23 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 pasteurella multocida
66d1kjqa3
not modelled 99.9 15 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
67d1gsoa3
not modelled 99.9 15 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
68d1pk8a2
not modelled 99.9 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Synapsin C-terminal domain
69d1uc8a2
not modelled 99.9 18 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Lysine biosynthesis enzyme LysX ATP-binding domain
70c3t9aA_
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
71c1gshA_
not modelled 99.9 13 PDB header:glutathione biosynthesis ligase
Chain: A: PDB Molecule:glutathione biosynthetic ligase;
PDBTitle: structure of escherichia coli glutathione synthetase at ph 7.5
72d1i7na2
not modelled 99.9 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Synapsin C-terminal domain
73c2qf7A_
not modelled 99.9 25 PDB header:ligase
Chain: A: PDB Molecule:pyruvate carboxylase protein;
PDBTitle: crystal structure of a complete multifunctional pyruvate carboxylase2 from rhizobium etli
74d1iowa1
not modelled 99.8 100 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:D-Alanine ligase N-terminal domain
75d1gsaa2
not modelled 99.6 11 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
76d1ehia1
not modelled 99.5 33 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:D-Alanine ligase N-terminal domain
77d1e4ea1
not modelled 99.5 35 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:D-Alanine ligase N-terminal domain
78c2r7mA_
not modelled 99.4 19 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
79c2cqyA_
not modelled 99.3 30 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 99.0 18 PDB header:ligase
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of an imp biosynthesis protein purp from2 thermococcus kodakaraensis
81c2nu9E_
not modelled 98.9 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
82c1wr2A_
not modelled 98.9 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ph1789;
PDBTitle: crystal structure of ph1788 from pyrococcus horikoshii ot3
83d1eucb2
not modelled 98.9 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Succinyl-CoA synthetase, beta-chain, N-terminal domain
84c1eucB_
not modelled 98.8 15 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
85c3tinA_
not modelled 98.8 19 PDB header:ligase
Chain: A: PDB Molecule:ttl protein;
PDBTitle: tubulin tyrosine ligase
86d1a9xa4
not modelled 98.7 26 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
87d2nu7b2
not modelled 98.7 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Succinyl-CoA synthetase, beta-chain, N-terminal domain
88d2pbza2
not modelled 98.6 19 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
89d1a9xa3
not modelled 98.3 28 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
90d1kjqa2
not modelled 97.8 21 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
91d1ulza2
not modelled 97.8 20 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
92c3mwdA_
not modelled 97.6 15 PDB header:transferase
Chain: A: PDB Molecule:atp-citrate synthase;
PDBTitle: truncated human atp-citrate lyase with citrate bound
93d2j9ga2
not modelled 97.6 26 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
94d1gsoa2
not modelled 97.2 14 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
95c3ktdC_
not modelled 96.1 18 PDB header:oxidoreductase
Chain: C: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of a putative prephenate dehydrogenase (cgl0226)2 from corynebacterium glutamicum atcc 13032 at 2.60 a resolution
96d1f0ya2
not modelled 95.8 26 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
97c3sc6F_
not modelled 95.6 17 PDB header:oxidoreductase
Chain: F: PDB Molecule:dtdp-4-dehydrorhamnose reductase;
PDBTitle: 2.65 angstrom resolution crystal structure of dtdp-4-dehydrorhamnose2 reductase (rfbd) from bacillus anthracis str. ames in complex with3 nadp
98d1w96a2
not modelled 95.6 20 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
99d1e5qa1
not modelled 95.4 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
100d1uc8a1
not modelled 95.4 13 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:Lysine biosynthesis enzyme LysX, N-terminal domain
101c3d8xB_
not modelled 95.3 11 PDB header:oxidoreductase
Chain: B: PDB Molecule:thioredoxin reductase 1;
PDBTitle: crystal structure of saccharomyces cerevisiae nadph dependent2 thioredoxin reductase 1
102d2jfga1
not modelled 95.2 11 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
103c2qx7A_
not modelled 95.0 21 PDB header:plant protein
Chain: A: PDB Molecule:eugenol synthase 1;
PDBTitle: structure of eugenol synthase from ocimum basilicum
104c3k96B_
not modelled 94.9 26 PDB header:oxidoreductase
Chain: B: PDB Molecule:glycerol-3-phosphate dehydrogenase [nad(p)+];
PDBTitle: 2.1 angstrom resolution crystal structure of glycerol-3-phosphate2 dehydrogenase (gpsa) from coxiella burnetii
105c3l6dB_
not modelled 94.8 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative oxidoreductase;
PDBTitle: crystal structure of putative oxidoreductase from pseudomonas putida2 kt2440
106d2hmva1
not modelled 94.4 25 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Potassium channel NAD-binding domain
107c3nhzA_
not modelled 94.4 18 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
108d1vkza2
not modelled 94.2 15 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
109d1lssa_
not modelled 94.1 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Potassium channel NAD-binding domain
110c1m75B_
not modelled 94.1 23 PDB header:oxidoreductase
Chain: B: PDB Molecule:3-hydroxyacyl-coa dehydrogenase;
PDBTitle: crystal structure of the n208s mutant of l-3-hydroxyacyl-2 coa dehydrogenase in complex with nad and acetoacetyl-coa
111c3eywA_
not modelled 94.1 17 PDB header:transport protein
Chain: A: PDB Molecule:c-terminal domain of glutathione-regulated potassium-efflux
PDBTitle: crystal structure of the c-terminal domain of e. coli kefc in complex2 with keff
112c3l4bG_
not modelled 94.0 6 PDB header:transport protein
Chain: G: PDB Molecule:trka k+ channel protien tm1088b;
PDBTitle: crystal structure of an octomeric two-subunit trka k+ channel ring2 gating assembly, tm1088a:tm1088b, from thermotoga maritima
113c2gr2A_
not modelled 93.9 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:ferredoxin reductase;
PDBTitle: crystal structure of ferredoxin reductase, bpha4 (oxidized form)
114d1k0ia1
not modelled 93.7 34 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD-linked reductases, N-terminal domain
115c3llvA_
not modelled 93.6 22 PDB header:nad(p) binding protein
Chain: A: PDB Molecule:exopolyphosphatase-related protein;
PDBTitle: the crystal structure of the nad(p)-binding domain of an2 exopolyphosphatase-related protein from archaeoglobus fulgidus to3 1.7a
116d1mvoa_
not modelled 93.6 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
117c3i3lA_
not modelled 93.5 29 PDB header:hydrolase
Chain: A: PDB Molecule:alkylhalidase cmls;
PDBTitle: crystal structure of cmls, a flavin-dependent halogenase
118c1phhA_
not modelled 93.5 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:p-hydroxybenzoate hydroxylase;
PDBTitle: crystal structure of p-hydroxybenzoate hydroxylase complexed with its2 reaction product 3,4-dihydroxybenzoate
119d1pfka_
not modelled 93.1 24 Fold:Phosphofructokinase
Superfamily:Phosphofructokinase
Family:Phosphofructokinase
120c2weuD_
not modelled 92.9 27 PDB header:antifungal protein
Chain: D: PDB Molecule:tryptophan 5-halogenase;
PDBTitle: crystal structure of tryptophan 5-halogenase (pyrh) complex2 with substrate tryptophan

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