Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP23538
DateThu Jan 5 11:39:36 GMT 2012
Unique Job ID9249341a7df1e565

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2olsA_
Top template information
PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate synthase;
PDBTitle: the crystal structure of the phosphoenolpyruvate synthase from2 neisseria meningitidis
Confidence and coverage
Confidence:100.0% Coverage: 91%
719 residues ( 91% 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  MSNNGSSPLVLWYNQLGMNDVDRVGGKNASLGEMITNLSGMGVSVPNGFATTADAFNQFL
Secondary structure 
SS confidence 
Disorder  ??????
?
??
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  DQSGVNQRIYELLDKTDIDDVTQLAKAGAQIRQWIIDTPFQPELENAIREAYAQLSADDE
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  NASFAVRSSATAEDMPDASFAGQQETFLNVQGFDAVLVAVKHVFASLFNDRAISYRVHQG
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  YDHRGVALSAGVQRMVRSDLASSGVMFSIDTESGFDQVVFITSAWGLGEMVVQGAVNPDE
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  FYVHKPTLAANRPAIVRRTMGSKKIRMVYAPTQEHGKQVKIEDVPQEQRDIFSLTNEEVQ
Secondary structure 
SS confidence 
Disorder 
????????
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  ELAKQAVQIEKHYGRPMDIEWAKDGHTGKLFIVQARPETVRSRGQVMERYTLHSQGKIIA
Secondary structure 
SS confidence 
Disorder 
????
????
???
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  EGRAIGHRIGAGPVKVIHDISEMNRIEPGDVLVTDMTDPDWEPIMKKASAIVTNRGGRTC
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  HAAIIARELGIPAVVGCGDATERMKDGENVTVSCAEGDTGYVYAELLEFSVKSSSVETMP
Secondary structure 
SS confidence 
Disorder 
???????
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  DLPLKVMMNVGNPDRAFDFACLPNEGVGLARLEFIINRMIGVHPRALLEFDDQEPQLQNE
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  IREMMKGFDSPREFYVGRLTEGIATLGAAFYPKRVIVRLSDFKSNEYANLVGGERYEPDE
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  ENPMLGFRGAGRYVSDSFRDCFALECEAVKRVRNDMGLTNVEIMIPFVRTVDQAKAVVEE
Secondary structure 
SS confidence 
Disorder  ?
??
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  LARQGLKRGENGLKIIMMCEIPSNALLAEQFLEYFDGFSIGSNDMTQLALGLDRDSGVVS
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  ELFDERNDAVKALLSMAIRAAKKQGKYVGICGQGPSDHEDFAAWLMEEGIDSLSLNPDTV
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........790..
Sequence  VQTWLSLAELKK
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 2ols chain A

3D model

Region: 9 - 789
Aligned: 719
Modelled: 737
Confidence: 100.0%
Identity: 68%
PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate synthase;
PDBTitle: the crystal structure of the phosphoenolpyruvate synthase from2 neisseria meningitidis

Phyre2

PDB 1h6z chain A

3D model

Region: 5 - 791
Aligned: 739
Modelled: 763
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: A: PDB Molecule:pyruvate phosphate dikinase;
PDBTitle: 3.0 a resolution crystal structure of glycosomal pyruvate2 phosphate dikinase from trypanosoma brucei

Phyre2

PDB 1kbl chain A

3D model

Region: 7 - 791
Aligned: 714
Modelled: 725
Confidence: 100.0%
Identity: 26%
PDB header:transferase
Chain: A: PDB Molecule:pyruvate phosphate dikinase;
PDBTitle: pyruvate phosphate dikinase

Phyre2

PDB 1vbh chain A

3D model

Region: 7 - 790
Aligned: 700
Modelled: 725
Confidence: 100.0%
Identity: 27%
PDB header:transferase
Chain: A: PDB Molecule:pyruvate,orthophosphate dikinase;
PDBTitle: pyruvate phosphate dikinase with bound mg-pep from maize

Phyre2

PDB 2hwg chain A

3D model

Region: 382 - 791
Aligned: 365
Modelled: 379
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of phosphorylated enzyme i of the2 phosphoenolpyruvate:sugar phosphotransferase system

Phyre2

PDB 2hro chain A

3D model

Region: 385 - 791
Aligned: 362
Modelled: 376
Confidence: 100.0%
Identity: 27%
PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of the full-lenght enzyme i of the pts system from2 staphylococcus carnosus

Phyre2

PDB 2bg5 chain C

3D model

Region: 469 - 791
Aligned: 282
Modelled: 292
Confidence: 100.0%
Identity: 26%
PDB header:transferase
Chain: C: PDB Molecule:phosphoenolpyruvate-protein kinase;
PDBTitle: crystal structure of the phosphoenolpyruvate-binding enzyme2 i-domain from the thermoanaerobacter tengcongensis pep:3 sugar phosphotransferase system (pts)

Phyre2

PDB 1h6z chain A domain 1

3D model

Region: 482 - 791
Aligned: 296
Modelled: 310
Confidence: 100.0%
Identity: 23%
Fold: TIM beta/alpha-barrel
Superfamily: Phosphoenolpyruvate/pyruvate domain
Family: Pyruvate phosphate dikinase, C-terminal domain

Phyre2

PDB 1vbg chain A domain 1

3D model

Region: 482 - 790
Aligned: 296
Modelled: 309
Confidence: 100.0%
Identity: 27%
Fold: TIM beta/alpha-barrel
Superfamily: Phosphoenolpyruvate/pyruvate domain
Family: Pyruvate phosphate dikinase, C-terminal domain

Phyre2

PDB 1kbl chain A domain 1

3D model

Region: 482 - 790
Aligned: 295
Modelled: 309
Confidence: 100.0%
Identity: 26%
Fold: TIM beta/alpha-barrel
Superfamily: Phosphoenolpyruvate/pyruvate domain
Family: Pyruvate phosphate dikinase, C-terminal domain

Phyre2

PDB 1kbl chain A domain 3

3D model

Region: 7 - 338
Aligned: 278
Modelled: 283
Confidence: 100.0%
Identity: 24%
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Family: Pyruvate phosphate dikinase, N-terminal domain

Phyre2

PDB 1vbg chain A domain 3

3D model

Region: 7 - 339
Aligned: 279
Modelled: 286
Confidence: 100.0%
Identity: 25%
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Family: Pyruvate phosphate dikinase, N-terminal domain

Phyre2

PDB 1h6z chain A domain 3

3D model

Region: 5 - 337
Aligned: 301
Modelled: 309
Confidence: 100.0%
Identity: 23%
Fold: ATP-grasp
Superfamily: Glutathione synthetase ATP-binding domain-like
Family: Pyruvate phosphate dikinase, N-terminal domain

Phyre2

PDB 1vbg chain A domain 2

3D model

Region: 347 - 470
Aligned: 121
Modelled: 124
Confidence: 99.9%
Identity: 29%
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: Phosphohistidine domain
Family: Pyruvate phosphate dikinase, central domain

Phyre2

PDB 1h6z chain A domain 2

3D model

Region: 346 - 469
Aligned: 121
Modelled: 124
Confidence: 99.9%
Identity: 30%
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: Phosphohistidine domain
Family: Pyruvate phosphate dikinase, central domain

Phyre2

PDB 1kbl chain A domain 2

3D model

Region: 345 - 465
Aligned: 118
Modelled: 121
Confidence: 99.9%
Identity: 28%
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: Phosphohistidine domain
Family: Pyruvate phosphate dikinase, central domain

Phyre2

PDB 1zym chain A domain 2

3D model

Region: 361 - 473
Aligned: 110
Modelled: 113
Confidence: 99.9%
Identity: 26%
Fold: The "swivelling" beta/beta/alpha domain
Superfamily: Phosphohistidine domain
Family: N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system

Phyre2

PDB 3qz6 chain A

3D model

Region: 490 - 791
Aligned: 204
Modelled: 223
Confidence: 99.8%
Identity: 18%
PDB header:lyase
Chain: A: PDB Molecule:hpch/hpai aldolase;
PDBTitle: the crystal structure of hpch/hpai aldolase from desulfitobacterium2 hafniense dcb-2

Phyre2

PDB 1eza chain A

3D model

Region: 383 - 473
Aligned: 88
Modelled: 91
Confidence: 99.8%
Identity: 26%
PDB header:phosphotransferase
Chain: A: PDB Molecule:enzyme i;
PDBTitle: amino terminal domain of enzyme i from escherichia coli nmr,2 restrained regularized mean structure

Phyre2

PDB 1dxe chain A

3D model

Region: 484 - 790
Aligned: 207
Modelled: 230
Confidence: 99.8%
Identity: 20%
Fold: TIM beta/alpha-barrel
Superfamily: Phosphoenolpyruvate/pyruvate domain
Family: HpcH/HpaI aldolase

Phyre2
1
c2olsA_
2
c1h6zA_
3
c1kblA_
4
c1vbhA_
5
c2hwgA_
6
c2hroA_
7
c2bg5C_
8
d1h6za1
9
d1vbga1
10
d1kbla1
11
d1kbla3
12
d1vbga3
13
d1h6za3
14
d1vbga2
15
d1h6za2
16
d1kbla2
17
d1zyma2
18
c3qz6A_
19
c1ezaA_
20
d1dxea_
21
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24
25
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2olsA_
100.0 68 PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate synthase;
PDBTitle: the crystal structure of the phosphoenolpyruvate synthase from2 neisseria meningitidis
2c1h6zA_
100.0 24 PDB header:transferase
Chain: A: PDB Molecule:pyruvate phosphate dikinase;
PDBTitle: 3.0 a resolution crystal structure of glycosomal pyruvate2 phosphate dikinase from trypanosoma brucei
3c1kblA_
100.0 26 PDB header:transferase
Chain: A: PDB Molecule:pyruvate phosphate dikinase;
PDBTitle: pyruvate phosphate dikinase
4c1vbhA_
100.0 27 PDB header:transferase
Chain: A: PDB Molecule:pyruvate,orthophosphate dikinase;
PDBTitle: pyruvate phosphate dikinase with bound mg-pep from maize
5c2hwgA_
100.0 25 PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of phosphorylated enzyme i of the2 phosphoenolpyruvate:sugar phosphotransferase system
6c2hroA_
100.0 27 PDB header:transferase
Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase;
PDBTitle: structure of the full-lenght enzyme i of the pts system from2 staphylococcus carnosus
7c2bg5C_
100.0 26 PDB header:transferase
Chain: C: PDB Molecule:phosphoenolpyruvate-protein kinase;
PDBTitle: crystal structure of the phosphoenolpyruvate-binding enzyme2 i-domain from the thermoanaerobacter tengcongensis pep:3 sugar phosphotransferase system (pts)
8d1h6za1
100.0 23 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate phosphate dikinase, C-terminal domain
9d1vbga1
100.0 27 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate phosphate dikinase, C-terminal domain
10d1kbla1
100.0 26 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate phosphate dikinase, C-terminal domain
11d1kbla3
100.0 24 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Pyruvate phosphate dikinase, N-terminal domain
12d1vbga3
100.0 25 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Pyruvate phosphate dikinase, N-terminal domain
13d1h6za3
100.0 23 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:Pyruvate phosphate dikinase, N-terminal domain
14d1vbga2
99.9 29 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:Phosphohistidine domain
Family:Pyruvate phosphate dikinase, central domain
15d1h6za2
99.9 30 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:Phosphohistidine domain
Family:Pyruvate phosphate dikinase, central domain
16d1kbla2
99.9 28 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:Phosphohistidine domain
Family:Pyruvate phosphate dikinase, central domain
17d1zyma2
99.9 26 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:Phosphohistidine domain
Family:N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system
18c3qz6A_
99.8 18 PDB header:lyase
Chain: A: PDB Molecule:hpch/hpai aldolase;
PDBTitle: the crystal structure of hpch/hpai aldolase from desulfitobacterium2 hafniense dcb-2
19c1ezaA_
99.8 26 PDB header:phosphotransferase
Chain: A: PDB Molecule:enzyme i;
PDBTitle: amino terminal domain of enzyme i from escherichia coli nmr,2 restrained regularized mean structure
20d1dxea_
99.8 20 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:HpcH/HpaI aldolase
21c3t07D_
not modelled 99.8 29 PDB header:transferase/transferase inhibitor
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of s. aureus pyruvate kinase in complex with a2 naturally occurring bis-indole alkaloid
22c2e28A_
not modelled 99.8 35 PDB header:transferase
Chain: A: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure analysis of pyruvate kinase from bacillus2 stearothermophilus
23c2v5jB_
not modelled 99.8 22 PDB header:lyase
Chain: B: PDB Molecule:2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase;
PDBTitle: apo class ii aldolase hpch
24d1izca_
not modelled 99.7 20 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:HpcH/HpaI aldolase
25c1izcA_
not modelled 99.7 20 PDB header:lyase
Chain: A: PDB Molecule:macrophomate synthase intermolecular diels-alderase;
PDBTitle: crystal structure analysis of macrophomate synthase
26c2vwtA_
not modelled 99.7 19 PDB header:lyase
Chain: A: PDB Molecule:yfau, 2-keto-3-deoxy sugar aldolase;
PDBTitle: crystal structure of yfau, a metal ion dependent class ii2 aldolase from escherichia coli k12 - mg-pyruvate product3 complex
27c1sgjB_
not modelled 99.2 23 PDB header:lyase
Chain: B: PDB Molecule:citrate lyase, beta subunit;
PDBTitle: crystal structure of citrate lyase beta subunit
28d1sgja_
not modelled 99.1 23 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:HpcH/HpaI aldolase
29c3qqwC_
not modelled 99.1 11 PDB header:lyase
Chain: C: PDB Molecule:putative citrate lyase;
PDBTitle: crystal structure of a hypothetical lyase (reut_b4148) from ralstonia2 eutropha jmp134 at 2.44 a resolution
30d1e0ta2
not modelled 99.1 17 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
31d1a3xa2
not modelled 99.0 19 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
32d2g50a2
not modelled 98.9 19 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
33d1pkla2
not modelled 98.9 20 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
34c3r4iB_
not modelled 98.8 13 PDB header:lyase
Chain: B: PDB Molecule:citrate lyase;
PDBTitle: crystal structure of a citrate lyase (bxe_b2899) from burkholderia2 xenovorans lb400 at 2.24 a resolution
35d1liua2
not modelled 98.8 20 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
36c1u5vA_
not modelled 98.7 19 PDB header:lyase
Chain: A: PDB Molecule:cite;
PDBTitle: structure of cite complexed with triphosphate group of atp2 form mycobacterium tuberculosis
37d1u5ha_
not modelled 98.6 20 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:HpcH/HpaI aldolase
38c1e0tD_
not modelled 98.1 22 PDB header:phosphotransferase
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: r292d mutant of e. coli pyruvate kinase
39c3pugA_
not modelled 97.8 25 PDB header:transferase
Chain: A: PDB Molecule:malate synthase;
PDBTitle: haloferax volcanii malate synthase native at 3mm glyoxylate
40c1a3wB_
not modelled 97.8 28 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase;
PDBTitle: pyruvate kinase from saccharomyces cerevisiae complexed with fbp, pg,2 mn2+ and k+
41c3e0vB_
not modelled 97.7 26 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pyruvate kinase from leishmania mexicana in2 complex with sulphate ions
42c3cuzA_
not modelled 97.7 12 PDB header:transferase
Chain: A: PDB Molecule:malate synthase a;
PDBTitle: atomic resolution structures of escherichia coli and2 bacillis anthracis malate synthase a: comparison with3 isoform g and implications for structure based drug design
43c1pklB_
not modelled 97.7 26 PDB header:transferase
Chain: B: PDB Molecule:protein (pyruvate kinase);
PDBTitle: the structure of leishmania pyruvate kinase
44c1t5aB_
not modelled 97.7 28 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase, m2 isozyme;
PDBTitle: human pyruvate kinase m2
45c3ma8A_
not modelled 97.7 21 PDB header:transferase
Chain: A: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of cgd1_2040, a pyruvate kinase from cryptosporidium2 parvum
46c1aqfB_
not modelled 97.6 28 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase;
PDBTitle: pyruvate kinase from rabbit muscle with mg, k, and l-2 phospholactate
47c2vgbB_
not modelled 97.6 32 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase isozymes r/l;
PDBTitle: human erythrocyte pyruvate kinase
48c3eoeC_
not modelled 97.6 27 PDB header:transferase
Chain: C: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pyruvate kinase from toxoplasma gondii, 55.m00007
49d1d8ca_
not modelled 97.1 13 Fold:TIM beta/alpha-barrel
Superfamily:Malate synthase G
Family:Malate synthase G
50c3khdC_
not modelled 97.1 24 PDB header:transferase
Chain: C: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pff1300w.
51c3cuxA_
not modelled 96.6 12 PDB header:transferase
Chain: A: PDB Molecule:malate synthase;
PDBTitle: atomic resolution structures of escherichia coli and2 bacillis anthracis malate synthase a: comparison with3 isoform g and implications for structure based drug design
52c3qjaA_
not modelled 92.9 14 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of the mycobacterium tuberculosis indole-3-glycerol2 phosphate synthase (trpc) in apo form
53d1n8ia_
not modelled 92.1 15 Fold:TIM beta/alpha-barrel
Superfamily:Malate synthase G
Family:Malate synthase G
54c2c3zA_
not modelled 92.0 11 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of a truncated variant of indole-3-2 glycerol phosphate synthase from sulfolobus solfataricus
55d2hi6a1
not modelled 92.0 26 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:LeuD/IlvD-like
Family:AF0055-like
56c3odmE_
not modelled 91.3 18 PDB header:lyase
Chain: E: PDB Molecule:phosphoenolpyruvate carboxylase;
PDBTitle: archaeal-type phosphoenolpyruvate carboxylase
57d1ea0a2
not modelled 91.2 15 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
58d1ofda2
not modelled 90.1 14 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
59d1vrda1
not modelled 90.0 15 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
60c2nv2U_
not modelled 89.3 24 PDB header:lyase/transferase
Chain: U: PDB Molecule:pyridoxal biosynthesis lyase pdxs;
PDBTitle: structure of the plp synthase complex pdx1/2 (yaad/e) from bacillus2 subtilis
61c2zbtB_
not modelled 89.0 25 PDB header:lyase
Chain: B: PDB Molecule:pyridoxal biosynthesis lyase pdxs;
PDBTitle: crystal structure of pyridoxine biosynthesis protein from thermus2 thermophilus hb8
62d1eepa_
not modelled 88.4 11 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
63d1jr1a1
not modelled 86.8 13 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
64c3femB_
not modelled 86.6 25 PDB header:biosynthetic protein, transferase
Chain: B: PDB Molecule:pyridoxine biosynthesis protein snz1;
PDBTitle: structure of the synthase subunit pdx1.1 (snz1) of plp synthase from2 saccharomyces cerevisiae
65c3ke8A_
not modelled 86.4 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-enyl diphosphate
PDBTitle: crystal structure of isph:hmbpp-complex
66c1m6vE_
not modelled 85.3 15 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
67d1a53a_
not modelled 83.9 11 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
68c2a7rD_
not modelled 83.1 10 PDB header:oxidoreductase
Chain: D: PDB Molecule:gmp reductase 2;
PDBTitle: crystal structure of human guanosine monophosphate2 reductase 2 (gmpr2)
69d1pvna1
not modelled 81.3 14 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
70c1vrdA_
not modelled 81.2 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine-5'-monophosphate dehydrogenase;
PDBTitle: crystal structure of inosine-5'-monophosphate dehydrogenase (tm1347)2 from thermotoga maritima at 2.18 a resolution
71d2cu0a1
not modelled 79.7 16 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
72d1zfja1
not modelled 75.8 11 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
73c2yzrB_
not modelled 73.2 35 PDB header:lyase
Chain: B: PDB Molecule:pyridoxal biosynthesis lyase pdxs;
PDBTitle: crystal structure of pyridoxine biosynthesis protein from2 methanocaldococcus jannaschii
74c3khjE_
not modelled 72.5 17 PDB header:oxidoreductase
Chain: E: PDB Molecule:inosine-5-monophosphate dehydrogenase;
PDBTitle: c. parvum inosine monophosphate dehydrogenase bound by inhibitor c64
75c3dnfB_
not modelled 72.0 20 PDB header:oxidoreductase
Chain: B: PDB Molecule:4-hydroxy-3-methylbut-2-enyl diphosphate reductase;
PDBTitle: structure of (e)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase,2 the terminal enzyme of the non-mevalonate pathway
76c3r2gA_
not modelled 70.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine 5'-monophosphate dehydrogenase;
PDBTitle: crystal structure of inosine 5' monophosphate dehydrogenase from2 legionella pneumophila
77c1jcnA_
not modelled 68.6 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine monophosphate dehydrogenase i;
PDBTitle: binary complex of human type-i inosine monophosphate dehydrogenase2 with 6-cl-imp
78c1wr2A_
not modelled 68.0 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ph1789;
PDBTitle: crystal structure of ph1788 from pyrococcus horikoshii ot3
79c3bleA_
not modelled 66.5 14 PDB header:transferase
Chain: A: PDB Molecule:citramalate synthase from leptospira interrogans;
PDBTitle: crystal structure of the catalytic domain of licms in2 complexed with malonate
80d1v7la_
not modelled 66.2 32 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:LeuD/IlvD-like
Family:LeuD-like
81c1lm1A_
not modelled 63.1 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:ferredoxin-dependent glutamate synthase;
PDBTitle: structural studies on the synchronization of catalytic centers in2 glutamate synthase: native enzyme
82c2zkrf_
not modelled 60.2 16 PDB header:ribosomal protein/rna
Chain: F: PDB Molecule:rna expansion segment es7 part iii;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
83c2a7nA_
not modelled 59.7 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:l(+)-mandelate dehydrogenase;
PDBTitle: crystal structure of the g81a mutant of the active chimera of (s)-2 mandelate dehydrogenase
84c3i12A_
not modelled 58.9 15 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
85d1j5ta_
not modelled 56.3 14 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
86c2vy9A_
not modelled 56.2 25 PDB header:gene regulation
Chain: A: PDB Molecule:anti-sigma-factor antagonist;
PDBTitle: molecular architecture of the stressosome, a signal2 integration and transduction hub
87c3iz5H_
not modelled 55.7 16 PDB header:ribosome
Chain: H: PDB Molecule:60s ribosomal protein l7a (l7ae);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
88d1snna_
not modelled 55.7 25 Fold:YrdC/RibB
Superfamily:YrdC/RibB
Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
89d1jcna1
not modelled 54.2 9 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
90c2vdcF_
not modelled 53.3 15 PDB header:oxidoreductase
Chain: F: PDB Molecule:glutamate synthase [nadph] large chain;
PDBTitle: the 9.5 a resolution structure of glutamate synthase from2 cryo-electron microscopy and its oligomerization behavior3 in solution: functional implications.
91d1rvga_
not modelled 53.1 19 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class II FBP aldolase
92c1me9A_
not modelled 51.8 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine-5'-monophosphate dehydrogenase;
PDBTitle: inosine monophosphate dehydrogenase (impdh) from2 tritrichomonas foetus with imp bound
93d2gp4a1
not modelled 50.8 20 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:LeuD/IlvD-like
Family:IlvD/EDD C-terminal domain-like
94c1w2wJ_
not modelled 49.6 26 PDB header:isomerase
Chain: J: PDB Molecule:5-methylthioribose-1-phosphate isomerase;
PDBTitle: crystal structure of yeast ypr118w, a methylthioribose-1-2 phosphate isomerase related to regulatory eif2b subunits
95c2pkpA_
not modelled 49.3 27 PDB header:lyase
Chain: A: PDB Molecule:homoaconitase small subunit;
PDBTitle: crystal structure of 3-isopropylmalate dehydratase (leud)2 from methhanocaldococcus jannaschii dsm2661 (mj1271)
96d1uuma_
not modelled 47.8 20 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
97d1i4na_
not modelled 47.7 17 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
98c2i80B_
not modelled 47.0 16 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
99d1th8b_
not modelled 46.9 10 Fold:SpoIIaa-like
Superfamily:SpoIIaa-like
Family:Anti-sigma factor antagonist SpoIIaa
100d1tb3a1
not modelled 46.7 15 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
101c2cu0B_
not modelled 46.6 19 PDB header:oxidoreductase
Chain: B: PDB Molecule:inosine-5'-monophosphate dehydrogenase;
PDBTitle: crystal structure of inosine-5'-monophosphate dehydrogenase from2 pyrococcus horikoshii ot3
102d1p4ca_
not modelled 45.7 13 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
103d1rpxa_
not modelled 45.4 14 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:D-ribulose-5-phosphate 3-epimerase
104d1gvfa_
not modelled 45.0 6 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class II FBP aldolase
105c3ffsC_
not modelled 43.9 14 PDB header:oxidoreductase
Chain: C: PDB Molecule:inosine-5-monophosphate dehydrogenase;
PDBTitle: the crystal structure of cryptosporidium parvum inosine-5'-2 monophosphate dehydrogenase
106c3bicA_
not modelled 43.7 15 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase, mitochondrial precursor;
PDBTitle: crystal structure of human methylmalonyl-coa mutase
107c2qr6A_
not modelled 41.6 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:imp dehydrogenase/gmp reductase;
PDBTitle: crystal structure of imp dehydrogenase/gmp reductase-like protein2 (np_599840.1) from corynebacterium glutamicum atcc 13032 kitasato at3 1.50 a resolution
108c3ln7A_
not modelled 40.9 23 PDB header:ligase
Chain: A: PDB Molecule:glutathione biosynthesis bifunctional protein gshab;
PDBTitle: crystal structure of a bifunctional glutathione synthetase from2 pasteurella multocida
109c3q58A_
not modelled 40.8 17 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
110c4a1eF_
not modelled 40.3 14 PDB header:ribosome
Chain: F: PDB Molecule:rpl7a;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1
111c3izcH_
not modelled 40.1 16 PDB header:ribosome
Chain: H: PDB Molecule:60s ribosomal protein rpl8 (l7ae);
PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
112d1a9xa5
not modelled 40.0 12 Fold:ATP-grasp
Superfamily:Glutathione synthetase ATP-binding domain-like
Family:BC ATP-binding domain-like
113c3oirA_
not modelled 37.7 14 PDB header:transport protein
Chain: A: PDB Molecule:sulfate transporter sulfate transporter family protein;
PDBTitle: crystal structure of sulfate transporter family protein from wolinella2 succinogenes
114d1piia2
not modelled 37.1 11 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
115c3ivuB_
not modelled 36.9 16 PDB header:transferase
Chain: B: PDB Molecule:homocitrate synthase, mitochondrial;
PDBTitle: homocitrate synthase lys4 bound to 2-og
116c2v82A_
not modelled 36.1 15 PDB header:lyase
Chain: A: PDB Molecule:2-dehydro-3-deoxy-6-phosphogalactonate aldolase;
PDBTitle: kdpgal complexed to kdpgal
117d1g57a_
not modelled 35.2 23 Fold:YrdC/RibB
Superfamily:YrdC/RibB
Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
118d3clsc1
not modelled 33.5 17 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Adenine nucleotide alpha hydrolases-like
Family:ETFP subunits
119d1tksa_
not modelled 32.8 18 Fold:YrdC/RibB
Superfamily:YrdC/RibB
Family:3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB
120c2o14A_
not modelled 32.6 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yxim;
PDBTitle: x-ray crystal structure of protein yxim_bacsu from bacillus2 subtilis. northeast structural genomics consortium target3 sr595

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