Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AES0
DateThu Jan 5 11:24:04 GMT 2012
Unique Job ID733290985eef1a41

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2ioaA_
Top template information
PDB header:ligase, hydrolase
Chain: A: PDB Molecule:bifunctional glutathionylspermidine
PDBTitle: e. coli bifunctional glutathionylspermidine2 synthetase/amidase incomplex with mg2+ and adp and3 phosphinate inhibitor
Confidence and coverage
Confidence:100.0% Coverage: 95%
589 residues ( 95% 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  MSKGTTSQDAPFGTLLGYAPGGVAIYSSDYSSLDPQEYEDDAVFRSYIDDEYMGHKWQCV
Secondary structure 
SS confidence 
Disorder  ???????
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  EFARRFLFLNYGVVFTDVGMAWEIFSLRFLREVVNDNILPLQAFPNGSPRAPVAGALLIW
Secondary structure 
SS confidence 
Disorder 
?
?????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  DKGGEFKDTGHVAIITQLHGNKVRIAEQNVIHSPLPQGQQWTRELEMVVENGCYTLKDTF
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  DDTTILGWMIQTEDTEYSLPQPEIAGELLKISGARLENKGQFDGKWLDEKDPLQNAYVQA
Secondary structure 
SS confidence 
Disorder 
???
?????
??
?????????????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  NGQVINQDPYHYYTITESAEQELIKATNELHLMYLHATDKVLKDDNLLALFDIPKILWPR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  LRLSWQRRRHHMITGRMDFCMDERGLKVYEYNADSASCHTEAGLILERWAEQGYKGNGFN
Secondary structure 
SS confidence 
Disorder 
?
??????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  PAEGLINELAGAWKHSRARPFVHIMQDKDIEENYHAQFMEQALHQAGFETRILRGLDELG
Secondary structure 
SS confidence 
Disorder  ?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  WDAAGQLIDGEGRLVNCVWKTWAWETAFDQIREVSDREFAAVPIRTGHPQNEVRLIDVLL
Secondary structure 
SS confidence 
Disorder 
?
???
??
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  RPEVLVFEPLWTVIPGNKAILPILWSLFPHHRYLLDTDFTVNDELVKTGYAVKPIAGRCG
Secondary structure 
SS confidence 
Disorder 
?
???????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  SNIDLVSHHEEVLDKTSGKFAEQKNIYQQLWCLPKVDGKYIQVCTFTVGGNYGGTCLRGD
Secondary structure 
SS confidence 
Disorder 
??
????????
????
Disorder confidence 
 
   .........610.........
Sequence  ESLVIKKESDIEPLIVVKK
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 2ioa chain A

3D model

Region: 10 - 618
Aligned: 589
Modelled: 609
Confidence: 100.0%
Identity: 100%
PDB header:ligase, hydrolase
Chain: A: PDB Molecule:bifunctional glutathionylspermidine
PDBTitle: e. coli bifunctional glutathionylspermidine2 synthetase/amidase incomplex with mg2+ and adp and3 phosphinate inhibitor

Phyre2

PDB 2vpm chain B

3D model

Region: 9 - 616
Aligned: 561
Modelled: 578
Confidence: 100.0%
Identity: 33%
PDB header:ligase
Chain: B: PDB Molecule:trypanothione synthetase;
PDBTitle: trypanothione synthetase

Phyre2

PDB 2io8 chain A domain 3

3D model

Region: 201 - 615
Aligned: 297
Modelled: 297
Confidence: 100.0%
Identity: 98%
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Family: Glutathionylspermidine synthase ATP-binding domain-like

Phyre2

PDB 2io8 chain A domain 2

3D model

Region: 10 - 200
Aligned: 183
Modelled: 191
Confidence: 100.0%
Identity: 98%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: CHAP domain

Phyre2

PDB 2io8 chain A domain 1

3D model

Region: 379 - 510
Aligned: 113
Modelled: 113
Confidence: 100.0%
Identity: 74%
Fold: PreATP-grasp domain
Superfamily: PreATP-grasp domain
Family: Glutathionylspermidine synthase substrate-binding domain-like

Phyre2

PDB 3n6x chain A

3D model

Region: 254 - 609
Aligned: 330
Modelled: 356
Confidence: 99.7%
Identity: 16%
PDB header:ligase
Chain: A: PDB Molecule:putative glutathionylspermidine synthase;
PDBTitle: crystal structure of a putative glutathionylspermidine synthase2 (mfla_0391) from methylobacillus flagellatus kt at 2.35 a resolution

Phyre2

PDB 2k3a chain A

3D model

Region: 14 - 164
Aligned: 127
Modelled: 135
Confidence: 98.6%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:chap domain protein;
PDBTitle: nmr solution structure of staphylococcus saprophyticus chap2 (cysteine, histidine-dependent amidohydrolases/peptidases)3 domain protein. northeast structural genomics consortium4 target syr11

Phyre2

PDB 2hgs chain A

3D model

Region: 255 - 616
Aligned: 330
Modelled: 340
Confidence: 98.4%
Identity: 18%
PDB header:amine/carboxylate ligase
Chain: A: PDB Molecule:protein (glutathione synthetase);
PDBTitle: human glutathione synthetase

Phyre2

PDB 3kal chain B

3D model

Region: 255 - 597
Aligned: 309
Modelled: 322
Confidence: 97.8%
Identity: 17%
PDB header:ligase
Chain: B: PDB Molecule:homoglutathione synthetase;
PDBTitle: structure of homoglutathione synthetase from glycine max in2 closed conformation with homoglutathione, adp, a sulfate3 ion, and three magnesium ions bound

Phyre2

PDB 1gsh chain A

3D model

Region: 395 - 600
Aligned: 173
Modelled: 183
Confidence: 97.4%
Identity: 14%
PDB header:glutathione biosynthesis ligase
Chain: A: PDB Molecule:glutathione biosynthetic ligase;
PDBTitle: structure of escherichia coli glutathione synthetase at ph 7.5

Phyre2

PDB 1pk8 chain D

3D model

Region: 463 - 615
Aligned: 147
Modelled: 153
Confidence: 97.1%
Identity: 14%
PDB header:membrane protein
Chain: D: PDB Molecule:rat synapsin i;
PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp

Phyre2

PDB 2wyo chain C

3D model

Region: 255 - 616
Aligned: 317
Modelled: 326
Confidence: 96.9%
Identity: 17%
PDB header:ligase
Chain: C: PDB Molecule:glutathione synthetase;
PDBTitle: trypanosoma brucei glutathione synthetase

Phyre2

PDB 2qb5 chain B

3D model

Region: 375 - 601
Aligned: 194
Modelled: 227
Confidence: 96.9%
Identity: 15%
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+

Phyre2

PDB 1uc8 chain B

3D model

Region: 381 - 605
Aligned: 180
Modelled: 199
Confidence: 96.8%
Identity: 16%
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

Phyre2

PDB 2p0a chain A

3D model

Region: 474 - 609
Aligned: 131
Modelled: 136
Confidence: 96.8%
Identity: 16%
PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin-3;
PDBTitle: the crystal structure of human synapsin iii (syn3) in complex with2 amppnp

Phyre2

PDB 1i7n chain A

3D model

Region: 475 - 609
Aligned: 129
Modelled: 135
Confidence: 96.7%
Identity: 14%
PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin ii;
PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain

Phyre2

PDB 1m0t chain B

3D model

Region: 255 - 534
Aligned: 251
Modelled: 260
Confidence: 96.3%
Identity: 20%
PDB header:ligase
Chain: B: PDB Molecule:glutathione synthetase;
PDBTitle: yeast glutathione synthase

Phyre2

PDB 1pk8 chain A domain 2

3D model

Region: 488 - 616
Aligned: 124
Modelled: 129
Confidence: 96.1%
Identity: 15%
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Family: Synapsin C-terminal domain

Phyre2

PDB 3t9a chain A

3D model

Region: 518 - 602
Aligned: 80
Modelled: 85
Confidence: 95.8%
Identity: 21%
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

Phyre2

PDB 3ln6 chain A

3D model

Region: 492 - 612
Aligned: 108
Modelled: 121
Confidence: 94.7%
Identity: 13%
PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 streptococcus agalactiae

Phyre2
1
c2ioaA_
2
c2vpmB_
3
d2io8a3
4
d2io8a2
5
d2io8a1
6
c3n6xA_
7
c2k3aA_
8
c2hgsA_
9
c3kalB_
10
c1gshA_
11
c1pk8D_
12
c2wyoC_
13
c2qb5B_
14
c1uc8B_
15
c2p0aA_
16
c1i7nA_
17
c1m0tB_
18
d1pk8a2
19
c3t9aA_
20
c3ln6A_
21
22
23
24
25
26
27
28
29
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31
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35
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2ioaA_
100.0 100 PDB header:ligase, hydrolase
Chain: A: PDB Molecule:bifunctional glutathionylspermidine
PDBTitle: e. coli bifunctional glutathionylspermidine2 synthetase/amidase incomplex with mg2+ and adp and3 phosphinate inhibitor
2c2vpmB_
100.0 33 PDB header:ligase
Chain: B: PDB Molecule:trypanothione synthetase;
PDBTitle: trypanothione synthetase
3d2io8a3
100.0 98 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Glutathionylspermidine synthase ATP-binding domain-like
4d2io8a2
100.0 98 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:CHAP domain
5d2io8a1
100.0 74 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:Glutathionylspermidine synthase substrate-binding domain-like
6c3n6xA_
99.7 16 PDB header:ligase
Chain: A: PDB Molecule:putative glutathionylspermidine synthase;
PDBTitle: crystal structure of a putative glutathionylspermidine synthase2 (mfla_0391) from methylobacillus flagellatus kt at 2.35 a resolution
7c2k3aA_
98.6 18 PDB header:hydrolase
Chain: A: PDB Molecule:chap domain protein;
PDBTitle: nmr solution structure of staphylococcus saprophyticus chap2 (cysteine, histidine-dependent amidohydrolases/peptidases)3 domain protein. northeast structural genomics consortium4 target syr11
8c2hgsA_
98.4 18 PDB header:amine/carboxylate ligase
Chain: A: PDB Molecule:protein (glutathione synthetase);
PDBTitle: human glutathione synthetase
9c3kalB_
97.8 17 PDB header:ligase
Chain: B: PDB Molecule:homoglutathione synthetase;
PDBTitle: structure of homoglutathione synthetase from glycine max in2 closed conformation with homoglutathione, adp, a sulfate3 ion, and three magnesium ions bound
10c1gshA_
97.4 14 PDB header:glutathione biosynthesis ligase
Chain: A: PDB Molecule:glutathione biosynthetic ligase;
PDBTitle: structure of escherichia coli glutathione synthetase at ph 7.5
11c1pk8D_
97.1 14 PDB header:membrane protein
Chain: D: PDB Molecule:rat synapsin i;
PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp
12c2wyoC_
96.9 17 PDB header:ligase
Chain: C: PDB Molecule:glutathione synthetase;
PDBTitle: trypanosoma brucei glutathione synthetase
13c2qb5B_
96.9 15 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+
14c1uc8B_
96.8 16 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
15c2p0aA_
96.8 16 PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin-3;
PDBTitle: the crystal structure of human synapsin iii (syn3) in complex with2 amppnp
16c1i7nA_
96.7 14 PDB header:neuropeptide
Chain: A: PDB Molecule:synapsin ii;
PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain
17c1m0tB_
96.3 20 PDB header:ligase
Chain: B: PDB Molecule:glutathione synthetase;
PDBTitle: yeast glutathione synthase
18d1pk8a2
96.1 15 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Synapsin C-terminal domain
19c3t9aA_
95.8 21 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
20c3ln6A_
94.7 13 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 streptococcus agalactiae
21d1i7na2
not modelled 94.4 15 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Synapsin C-terminal domain
22d1gsaa2
not modelled 93.6 20 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
23c3ln7A_
not modelled 93.0 14 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 pasteurella multocida
24c3bg5C_
not modelled 90.5 18 PDB header:ligase
Chain: C: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase
25c3lp8A_
not modelled 89.7 25 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine-glycine ligase;
PDBTitle: crystal structure of phosphoribosylamine-glycine ligase from2 ehrlichia chaffeensis
26c1kjjA_
not modelled 89.4 12 PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s
27c2yyaB_
not modelled 89.2 20 PDB header:ligase
Chain: B: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of gar synthetase from aquifex aeolicus
28c1vkzA_
not modelled 88.5 14 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
29c2hjwA_
not modelled 88.0 17 PDB header:ligase
Chain: A: PDB Molecule:acetyl-coa carboxylase 2;
PDBTitle: crystal structure of the bc domain of acc2
30c2xd4A_
not modelled 87.7 19 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: nucleotide-bound structures of bacillus subtilis glycinamide2 ribonucleotide synthetase
31d2if6a1
not modelled 87.4 17 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:YiiX-like
32c1ulzA_
not modelled 87.0 14 PDB header:ligase
Chain: A: PDB Molecule:pyruvate carboxylase n-terminal domain;
PDBTitle: crystal structure of the biotin carboxylase subunit of pyruvate2 carboxylase
33c2i80B_
not modelled 86.9 18 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
34c2ip4A_
not modelled 86.2 18 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase;
PDBTitle: crystal structure of glycinamide ribonucleotide synthetase from2 thermus thermophilus hb8
35c3tinA_
not modelled 86.1 12 PDB header:ligase
Chain: A: PDB Molecule:ttl protein;
PDBTitle: tubulin tyrosine ligase
36c1ehiB_
not modelled 85.2 20 PDB header:ligase
Chain: B: PDB Molecule:d-alanine:d-lactate ligase;
PDBTitle: d-alanine:d-lactate ligase (lmddl2) of vancomycin-resistant2 leuconostoc mesenteroides
37c2dzdB_
not modelled 84.3 12 PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of the biotin carboxylase domain of2 pyruvate carboxylase
38c2vpqA_
not modelled 84.0 12 PDB header:ligase
Chain: A: PDB Molecule:acetyl-coa carboxylase;
PDBTitle: crystal structure of biotin carboxylase from s. aureus2 complexed with amppnp
39c3se7A_
not modelled 83.6 19 PDB header:ligase
Chain: A: PDB Molecule:vana;
PDBTitle: ancient vana
40c3gidB_
not modelled 81.8 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
41c2dlnA_
not modelled 81.8 23 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
42c2pvpB_
not modelled 81.7 19 PDB header:ligase
Chain: B: PDB Molecule:d-alanine-d-alanine ligase;
PDBTitle: crystal structure of d-alanine-d-alanine ligase from helicobacter2 pylori
43c3tqtB_
not modelled 80.7 16 PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: structure of the d-alanine-d-alanine ligase from coxiella burnetii
44c3ouzA_
not modelled 80.2 10 PDB header:ligase
Chain: A: PDB Molecule:biotin carboxylase;
PDBTitle: crystal structure of biotin carboxylase-adp complex from campylobacter2 jejuni
45c3g8cB_
not modelled 79.7 14 PDB header:ligase
Chain: B: PDB Molecule:biotin carboxylase;
PDBTitle: crystal stucture of biotin carboxylase in complex with2 biotin, bicarbonate, adp and mg ion
46c3lwbA_
not modelled 78.5 22 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
47d1gsaa1
not modelled 78.3 11 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:Prokaryotic glutathione synthetase, N-terminal domain
48d3etja3
not modelled 76.6 16 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
49d1e4ea2
not modelled 75.3 13 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
50c2zdqA_
not modelled 75.3 10 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
51c3r23B_
not modelled 75.0 16 PDB header:ligase
Chain: B: PDB Molecule:d-alanine--d-alanine ligase;
PDBTitle: crystal structure of d-alanine--d-alanine ligase from bacillus2 anthracis
52d1uc8a2
not modelled 74.8 27 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Lysine biosynthesis enzyme LysX ATP-binding domain
53d1fs2b1
not modelled 74.6 20 Fold:Skp1 dimerisation domain-like
Superfamily:Skp1 dimerisation domain-like
Family:Skp1 dimerisation domain-like
54d1gsoa3
not modelled 74.0 30 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
55c1w96B_
not modelled 72.8 20 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
56c2k1gA_
not modelled 72.7 22 PDB header:lipoprotein
Chain: A: PDB Molecule:lipoprotein spr;
PDBTitle: solution nmr structure of lipoprotein spr from escherichia coli k12.2 northeast structural genomics target er541-37-162
57c3i12A_
not modelled 72.5 11 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
58d1iowa2
not modelled 71.6 24 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
59c3e5nA_
not modelled 71.1 25 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
60d1kjqa3
not modelled 69.8 5 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
61d1ehia2
not modelled 69.6 24 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:ATP-binding domain of peptide synthetases
62d2j9ga3
not modelled 68.0 20 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
63c3kw0D_
not modelled 67.0 33 PDB header:hydrolase
Chain: D: PDB Molecule:cysteine peptidase;
PDBTitle: crystal structure of cysteine peptidase (np_982244.1) from bacillus2 cereus atcc 10987 at 2.50 a resolution
64c3df7A_
not modelled 64.5 14 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
65c1e4eB_
not modelled 64.5 13 PDB header:ligase
Chain: B: PDB Molecule:vancomycin/teicoplanin a-type resistance protein vana;
PDBTitle: d-alanyl-d-lacate ligase
66d1vkza3
not modelled 63.6 17 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
67d1w96a3
not modelled 62.8 13 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
68c2cqyA_
not modelled 60.6 16 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
69c2gpwC_
not modelled 59.8 13 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.
70c3pbiA_
not modelled 59.3 27 PDB header:hydrolase
Chain: A: PDB Molecule:invasion protein;
PDBTitle: structure of the peptidoglycan hydrolase ripb (rv1478) from2 mycobacterium tuberculosis at 1.6 resolution
71c3k3pA_
not modelled 58.6 18 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
72d2evra2
not modelled 58.4 27 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:NlpC/P60
73c3orqA_
not modelled 55.0 8 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
74d1nexa1
not modelled 53.3 19 Fold:Skp1 dimerisation domain-like
Superfamily:Skp1 dimerisation domain-like
Family:Skp1 dimerisation domain-like
75d1a9xa6
not modelled 51.3 8 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
76d1vbva1
not modelled 49.3 23 Fold:SH3-like barrel
Superfamily:YccV-like
Family:YccV-like
77d2ovra1
not modelled 49.0 21 Fold:Skp1 dimerisation domain-like
Superfamily:Skp1 dimerisation domain-like
Family:Skp1 dimerisation domain-like
78c2ys6A_
not modelled 47.1 35 PDB header:ligase
Chain: A: PDB Molecule:phosphoribosylglycinamide synthetase;
PDBTitle: crystal structure of gar synthetase from geobacillus kaustophilus
79c2fg0B_
not modelled 46.6 29 PDB header:hydrolase
Chain: B: PDB Molecule:cog0791: cell wall-associated hydrolases (invasion-
PDBTitle: crystal structure of a putative gamma-d-glutamyl-l-diamino acid2 endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.793 a resolution
80c2p1nD_
not modelled 45.5 24 PDB header:signaling protein
Chain: D: PDB Molecule:skp1-like protein 1a;
PDBTitle: mechanism of auxin perception by the tir1 ubiqutin ligase
81c1z2pX_
not modelled 45.0 19 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
82d1a9xa5
not modelled 42.0 8 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
83c1nexC_
not modelled 42.0 18 PDB header:ligase, cell cycle
Chain: C: PDB Molecule:centromere dna-binding protein complex cbf3
PDBTitle: crystal structure of scskp1-sccdc4-cpd peptide complex
84c3s4wB_
not modelled 40.9 32 PDB header:dna binding protein
Chain: B: PDB Molecule:fanconi anemia group d2 protein homolog;
PDBTitle: structure of the fanci-fancd2 complex
85c2dwcB_
not modelled 40.7 4 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
86d2hgsa4
not modelled 40.3 19 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Eukaryotic glutathione synthetase ATP-binding domain
87c3n6rK_
not modelled 39.6 25 PDB header:ligase
Chain: K: PDB Molecule:propionyl-coa carboxylase, alpha subunit;
PDBTitle: crystal structure of the holoenzyme of propionyl-coa carboxylase (pcc)
88c3i86A_
not modelled 39.2 17 PDB header:hydrolase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of the p60 domain from m. avium subspecies2 paratuberculosis antigen map1204
89d2auaa1
not modelled 38.0 40 Fold:ADP-ribosylation
Superfamily:ADP-ribosylation
Family:BC2332-like
90d1irza_
not modelled 37.8 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:GARP response regulators
91c2xivA_
not modelled 36.8 18 PDB header:structural protein
Chain: A: PDB Molecule:hypothetical invasion protein;
PDBTitle: structure of rv1477, hypothetical invasion protein of2 mycobacterium tuberculosis
92d2r85a2
not modelled 35.5 13 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
93c3gt2A_
not modelled 34.6 19 PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of the p60 domain from m. avium2 paratuberculosis antigen map1272c
94c1gsoA_
not modelled 32.4 33 PDB header:ligase
Chain: A: PDB Molecule:protein (glycinamide ribonucleotide synthetase);
PDBTitle: glycinamide ribonucleotide synthetase (gar-syn) from e.2 coli.
95c3al6A_
not modelled 32.1 10 PDB header:unknown function
Chain: A: PDB Molecule:jmjc domain-containing protein c2orf60;
PDBTitle: crystal structure of human tyw5
96d2r7ka2
not modelled 32.0 21 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:PurP ATP-binding domain-like
97d2oo3a1
not modelled 31.8 19 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:LPG1296-like
98c3kopB_
not modelled 30.9 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of protein with a cyclophilin-like fold2 (yp_831253.1) from arthrobacter sp. fb24 at 1.90 a resolution
99c2qk4A_
not modelled 30.7 26 PDB header:ligase
Chain: A: PDB Molecule:trifunctional purine biosynthetic protein adenosine-3;
PDBTitle: human glycinamide ribonucleotide synthetase
100c3h41A_
not modelled 28.8 17 PDB header:hydrolase
Chain: A: PDB Molecule:nlp/p60 family protein;
PDBTitle: crystal structure of a nlpc/p60 family protein (bce_2878) from2 bacillus cereus atcc 10987 at 1.79 a resolution
101d1saza1
not modelled 27.0 18 Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:Acetokinase-like
102c3etjB_
not modelled 26.2 16 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase atpase
PDBTitle: crystal structure e. coli purk in complex with mg, adp, and2 pi
103d1vlya1
not modelled 25.2 27 Fold:Elongation factor/aminomethyltransferase common domain
Superfamily:Aminomethyltransferase beta-barrel domain
Family:Aminomethyltransferase beta-barrel domain
104c3heiI_
not modelled 25.0 18 PDB header:transferase/signaling protein
Chain: I: PDB Molecule:ephrin type-a receptor 2;
PDBTitle: ligand recognition by a-class eph receptors: crystal structures of the2 epha2 ligand-binding domain and the epha2/ephrin-a1 complex
105d1ulza3
not modelled 24.0 21 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
106c3q2oB_
not modelled 24.0 5 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase
107c2kytA_
not modelled 23.8 35 PDB header:hydrolase
Chain: A: PDB Molecule:group xvi phospholipase a2;
PDBTitle: solution struture of the h-rev107 n-terminal domain
108d1t3da_
not modelled 23.6 15 Fold:Single-stranded left-handed beta-helix
Superfamily:Trimeric LpxA-like enzymes
Family:Serine acetyltransferase
109c2z04A_
not modelled 23.6 10 PDB header:lyase
Chain: A: PDB Molecule:phosphoribosylaminoimidazole carboxylase atpase
PDBTitle: crystal structure of phosphoribosylaminoimidazole2 carboxylase atpase subunit from aquifex aeolicus
110c3kvpB_
not modelled 23.6 57 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein ymzc;
PDBTitle: crystal structure of uncharacterized protein ymzc precursor2 from bacillus subtilis, northeast structural genomics3 consortium target sr378a
111c2pn1A_
not modelled 22.8 9 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
112c2ovqA_
not modelled 21.5 21 PDB header:transcription/cell cycle
Chain: A: PDB Molecule:s-phase kinase-associated protein 1a;
PDBTitle: structure of the skp1-fbw7-cyclinedegc complex
113c2p1gA_
not modelled 20.6 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative xylanase;
PDBTitle: crystal structure of a putative xylanase from bacteroides fragilis

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