Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP14900
DateThu Jan 5 11:34:07 GMT 2012
Unique Job ID14fc734943229492

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3uagA_
Top template information
PDB header:ligase
Chain: A: PDB Molecule:protein (udp-n-acetylmuramoyl-l-alanine:d-
PDBTitle: udp-n-acetylmuramoyl-l-alanine:d-glutamate ligase
Confidence and coverage
Confidence:100.0% Coverage: 98%
429 residues ( 98% 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  MADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLND
Secondary structure 
SS confidence 
Disorder  ????
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  EWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVT
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  TLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNV
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  TEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  NHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGL
Secondary structure 
SS confidence 
Disorder 
??
?
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  PHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  NGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQF
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430........
Sequence  KNFEQRGNEFARLAKELG
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 3uag chain A

3D model

Region: 2 - 438
Aligned: 429
Modelled: 437
Confidence: 100.0%
Identity: 98%
PDB header:ligase
Chain: A: PDB Molecule:protein (udp-n-acetylmuramoyl-l-alanine:d-
PDBTitle: udp-n-acetylmuramoyl-l-alanine:d-glutamate ligase

Phyre2

PDB 3lk7 chain A

3D model

Region: 1 - 437
Aligned: 432
Modelled: 437
Confidence: 100.0%
Identity: 29%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine--d-glutamate ligase;
PDBTitle: the crystal structure of udp-n-acetylmuramoylalanine-d-2 glutamate (murd) ligase from streptococcus agalactiae to3 1.5a

Phyre2

PDB 2f00 chain A

3D model

Region: 1 - 420
Aligned: 417
Modelled: 420
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate--l-alanine ligase;
PDBTitle: escherichia coli murc

Phyre2

PDB 3hn7 chain A

3D model

Region: 6 - 437
Aligned: 420
Modelled: 427
Confidence: 100.0%
Identity: 18%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: crystal structure of a murein peptide ligase mpl (psyc_0032) from2 psychrobacter arcticus 273-4 at 1.65 a resolution

Phyre2

PDB 1j6u chain A

3D model

Region: 6 - 426
Aligned: 407
Modelled: 421
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-alanine ligase murc;
PDBTitle: crystal structure of udp-n-acetylmuramate-alanine ligase2 murc (tm0231) from thermotoga maritima at 2.3 a resolution

Phyre2

PDB 1gqq chain A

3D model

Region: 7 - 426
Aligned: 393
Modelled: 401
Confidence: 100.0%
Identity: 19%
PDB header:cell wall biosynthesis
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: murc - crystal structure of the apo-enzyme from haemophilus2 influenzae

Phyre2

PDB 3eag chain A

3D model

Region: 5 - 302
Aligned: 297
Modelled: 298
Confidence: 100.0%
Identity: 20%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamyl-meso-
PDBTitle: the crystal structure of udp-n-acetylmuramate:l-alanyl-gamma-d-2 glutamyl-meso-diaminopimelate ligase (mpl) from neisseria3 meningitides

Phyre2

PDB 2am1 chain A

3D model

Region: 98 - 437
Aligned: 327
Modelled: 337
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine-d-glutamyl-lysine-d-alanyl-d-
PDBTitle: sp protein ligand 1

Phyre2

PDB 1e8c chain B

3D model

Region: 64 - 437
Aligned: 370
Modelled: 372
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: B: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamate--2,6-
PDBTitle: structure of mure the udp-n-acetylmuramyl tripeptide2 synthetase from e. coli

Phyre2

PDB 1gg4 chain A

3D model

Region: 18 - 437
Aligned: 396
Modelled: 419
Confidence: 100.0%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-
PDBTitle: crystal structure of escherichia coli udpmurnac-tripeptide2 d-alanyl-d-alanine-adding enzyme (murf) at 2.3 angstrom3 resolution

Phyre2

PDB 2wtz chain C

3D model

Region: 101 - 411
Aligned: 287
Modelled: 311
Confidence: 100.0%
Identity: 24%
PDB header:ligase
Chain: C: PDB Molecule:udp-n-acetylmuramoyl-l-alanyl-d-glutamate-
PDBTitle: mure ligase of mycobacterium tuberculosis

Phyre2

PDB 2vos chain A

3D model

Region: 74 - 419
Aligned: 330
Modelled: 345
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase protein folc;
PDBTitle: mycobacterium tuberculosis folylpolyglutamate synthase2 complexed with adp

Phyre2

PDB 1w78 chain A

3D model

Region: 72 - 417
Aligned: 326
Modelled: 345
Confidence: 100.0%
Identity: 22%
PDB header:synthase
Chain: A: PDB Molecule:folc bifunctional protein;
PDBTitle: e.coli folc in complex with dhpp and adp

Phyre2

PDB 2gc6 chain A

3D model

Region: 101 - 419
Aligned: 299
Modelled: 318
Confidence: 100.0%
Identity: 16%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase;
PDBTitle: s73a mutant of l. casei fpgs

Phyre2

PDB 3n2a chain A

3D model

Region: 72 - 438
Aligned: 333
Modelled: 361
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:bifunctional folylpolyglutamate synthase/dihydrofolate
PDBTitle: crystal structure of bifunctional folylpolyglutamate2 synthase/dihydrofolate synthase from yersinia pestis co92

Phyre2

PDB 1o5z chain A

3D model

Region: 75 - 419
Aligned: 316
Modelled: 335
Confidence: 100.0%
Identity: 22%
PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase/dihydrofolate synthase;
PDBTitle: crystal structure of folylpolyglutamate synthase (tm0166) from2 thermotoga maritima at 2.10 a resolution

Phyre2

PDB 2jfg chain A domain 3

3D model

Region: 95 - 298
Aligned: 203
Modelled: 204
Confidence: 100.0%
Identity: 97%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2

PDB 2jfg chain A domain 2

3D model

Region: 299 - 438
Aligned: 140
Modelled: 140
Confidence: 100.0%
Identity: 100%
Fold: MurD-like peptide ligases, peptide-binding domain
Superfamily: MurD-like peptide ligases, peptide-binding domain
Family: MurCDEF C-terminal domain

Phyre2

PDB 1p3d chain A domain 3

3D model

Region: 95 - 298
Aligned: 203
Modelled: 198
Confidence: 100.0%
Identity: 19%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2

PDB 1e8c chain A domain 3

3D model

Region: 103 - 299
Aligned: 196
Modelled: 197
Confidence: 100.0%
Identity: 27%
Fold: Ribokinase-like
Superfamily: MurD-like peptide ligases, catalytic domain
Family: MurCDEF

Phyre2
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c3uagA_
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c3lk7A_
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c2f00A_
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c3hn7A_
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c1j6uA_
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c1gqqA_
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c3eagA_
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c2am1A_
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c1e8cB_
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c1gg4A_
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c2wtzC_
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c2vosA_
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c1w78A_
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c2gc6A_
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d2jfga3
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d1p3da3
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3uagA_
100.0 98 PDB header:ligase
Chain: A: PDB Molecule:protein (udp-n-acetylmuramoyl-l-alanine:d-
PDBTitle: udp-n-acetylmuramoyl-l-alanine:d-glutamate ligase
2c3lk7A_
100.0 29 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine--d-glutamate ligase;
PDBTitle: the crystal structure of udp-n-acetylmuramoylalanine-d-2 glutamate (murd) ligase from streptococcus agalactiae to3 1.5a
3c2f00A_
100.0 18 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate--l-alanine ligase;
PDBTitle: escherichia coli murc
4c3hn7A_
100.0 18 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: crystal structure of a murein peptide ligase mpl (psyc_0032) from2 psychrobacter arcticus 273-4 at 1.65 a resolution
5c1j6uA_
100.0 22 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate-alanine ligase murc;
PDBTitle: crystal structure of udp-n-acetylmuramate-alanine ligase2 murc (tm0231) from thermotoga maritima at 2.3 a resolution
6c1gqqA_
100.0 19 PDB header:cell wall biosynthesis
Chain: A: PDB Molecule:udp-n-acetylmuramate-l-alanine ligase;
PDBTitle: murc - crystal structure of the apo-enzyme from haemophilus2 influenzae
7c3eagA_
100.0 20 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamyl-meso-
PDBTitle: the crystal structure of udp-n-acetylmuramate:l-alanyl-gamma-d-2 glutamyl-meso-diaminopimelate ligase (mpl) from neisseria3 meningitides
8c2am1A_
100.0 22 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanine-d-glutamyl-lysine-d-alanyl-d-
PDBTitle: sp protein ligand 1
9c1e8cB_
100.0 22 PDB header:ligase
Chain: B: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamate--2,6-
PDBTitle: structure of mure the udp-n-acetylmuramyl tripeptide2 synthetase from e. coli
10c1gg4A_
100.0 21 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-
PDBTitle: crystal structure of escherichia coli udpmurnac-tripeptide2 d-alanyl-d-alanine-adding enzyme (murf) at 2.3 angstrom3 resolution
11c2wtzC_
100.0 24 PDB header:ligase
Chain: C: PDB Molecule:udp-n-acetylmuramoyl-l-alanyl-d-glutamate-
PDBTitle: mure ligase of mycobacterium tuberculosis
12c2vosA_
100.0 22 PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase protein folc;
PDBTitle: mycobacterium tuberculosis folylpolyglutamate synthase2 complexed with adp
13c1w78A_
100.0 22 PDB header:synthase
Chain: A: PDB Molecule:folc bifunctional protein;
PDBTitle: e.coli folc in complex with dhpp and adp
14c2gc6A_
100.0 16 PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase;
PDBTitle: s73a mutant of l. casei fpgs
15c3n2aA_
100.0 22 PDB header:ligase
Chain: A: PDB Molecule:bifunctional folylpolyglutamate synthase/dihydrofolate
PDBTitle: crystal structure of bifunctional folylpolyglutamate2 synthase/dihydrofolate synthase from yersinia pestis co92
16c1o5zA_
100.0 22 PDB header:ligase
Chain: A: PDB Molecule:folylpolyglutamate synthase/dihydrofolate synthase;
PDBTitle: crystal structure of folylpolyglutamate synthase (tm0166) from2 thermotoga maritima at 2.10 a resolution
17d2jfga3
100.0 97 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
18d2jfga2
100.0 100 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
19d1p3da3
100.0 19 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
20d1e8ca3
100.0 27 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
21d1j6ua3
not modelled 100.0 32 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
22d2gc6a2
not modelled 100.0 15 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:Folylpolyglutamate synthetase
23d1gg4a4
not modelled 100.0 22 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:MurCDEF
24d1o5za2
not modelled 100.0 20 Fold:Ribokinase-like
Superfamily:MurD-like peptide ligases, catalytic domain
Family:Folylpolyglutamate synthetase
25d1gg4a1
not modelled 99.7 18 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
26d2jfga1
not modelled 99.7 100 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
27d1j6ua1
not modelled 99.7 14 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
28d1p3da1
not modelled 99.7 19 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
29d1e8ca2
not modelled 99.6 18 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
30c3mvnA_
not modelled 99.5 16 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamayl-medo-
PDBTitle: crystal structure of a domain from a putative udp-n-acetylmuramate:l-2 alanyl-gamma-d-glutamayl-medo-diaminopimelate ligase from haemophilus3 ducreyi 35000hp
31d1p3da2
not modelled 99.5 17 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
32d1j6ua2
not modelled 99.1 11 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:MurCDEF C-terminal domain
33d1o5za1
not modelled 98.9 25 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:Folylpolyglutamate synthetase, C-terminal domain
34d2gc6a1
not modelled 98.7 20 Fold:MurD-like peptide ligases, peptide-binding domain
Superfamily:MurD-like peptide ligases, peptide-binding domain
Family:Folylpolyglutamate synthetase, C-terminal domain
35d1pjqa1
not modelled 98.6 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Siroheme synthase N-terminal domain-like
36c3d4oA_
not modelled 98.2 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:dipicolinate synthase subunit a;
PDBTitle: crystal structure of dipicolinate synthase subunit a (np_243269.1)2 from bacillus halodurans at 2.10 a resolution
37c3gg2B_
not modelled 97.9 17 PDB header:oxidoreductase
Chain: B: PDB Molecule:sugar dehydrogenase, udp-glucose/gdp-mannose
PDBTitle: crystal structure of udp-glucose 6-dehydrogenase from2 porphyromonas gingivalis bound to product udp-glucuronate
38c2y0dB_
not modelled 97.9 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:udp-glucose dehydrogenase;
PDBTitle: bcec mutation y10k
39c3cumA_
not modelled 97.9 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:probable 3-hydroxyisobutyrate dehydrogenase;
PDBTitle: crystal structure of a possible 3-hydroxyisobutyrate dehydrogenase2 from pseudomonas aeruginosa pao1
40c1mv8A_
not modelled 97.8 23 PDB header:oxidoreductase
Chain: A: PDB Molecule:gdp-mannose 6-dehydrogenase;
PDBTitle: 1.55 a crystal structure of a ternary complex of gdp-mannose2 dehydrogenase from psuedomonas aeruginosa
41c2rirA_
not modelled 97.8 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:dipicolinate synthase, a chain;
PDBTitle: crystal structure of dipicolinate synthase, a chain, from bacillus2 subtilis
42c1pjtB_
not modelled 97.8 17 PDB header:transferase/oxidoreductase/lyase
Chain: B: PDB Molecule:siroheme synthase;
PDBTitle: the structure of the ser128ala point-mutant variant of cysg,2 the multifunctional3 methyltransferase/dehydrogenase/ferrochelatase for4 siroheme synthesis
43c1gdhA_
not modelled 97.8 14 PDB header:oxidoreductase(choh (d)-nad(p)+ (a))
Chain: A: PDB Molecule:d-glycerate dehydrogenase;
PDBTitle: crystal structure of a nad-dependent d-glycerate2 dehydrogenase at 2.4 angstroms resolution
44d3cuma2
not modelled 97.8 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
45c3dhyC_
not modelled 97.8 21 PDB header:hydrolase
Chain: C: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structures of mycobacterium tuberculosis s-adenosyl-l-2 homocysteine hydrolase in ternary complex with substrate and3 inhibitors
46c3dfzB_
not modelled 97.8 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:precorrin-2 dehydrogenase;
PDBTitle: sirc, precorrin-2 dehydrogenase
47d1nyta1
not modelled 97.8 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
48c3gvpB_
not modelled 97.8 19 PDB header:hydrolase
Chain: B: PDB Molecule:adenosylhomocysteinase 3;
PDBTitle: human sahh-like domain of human adenosylhomocysteinase 3
49c2g5cD_
not modelled 97.8 19 PDB header:oxidoreductase
Chain: D: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from aquifex aeolicus
50c1d4fD_
not modelled 97.7 20 PDB header:hydrolase
Chain: D: PDB Molecule:s-adenosylhomocysteine hydrolase;
PDBTitle: crystal structure of recombinant rat-liver d244e mutant s-2 adenosylhomocysteine hydrolase
51d1mx3a1
not modelled 97.7 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
52d2naca1
not modelled 97.7 14 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
53c3g79A_
not modelled 97.7 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:ndp-n-acetyl-d-galactosaminuronic acid dehydrogenase;
PDBTitle: crystal structure of ndp-n-acetyl-d-galactosaminuronic acid2 dehydrogenase from methanosarcina mazei go1
54c2hk8B_
not modelled 97.7 17 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from aquifex2 aeolicus at 2.35 angstrom resolution
55c1np3B_
not modelled 97.7 23 PDB header:oxidoreductase
Chain: B: PDB Molecule:ketol-acid reductoisomerase;
PDBTitle: crystal structure of class i acetohydroxy acid isomeroreductase from2 pseudomonas aeruginosa
56c3oneA_
not modelled 97.7 19 PDB header:hydrolase/hydrolase substrate
Chain: A: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of lupinus luteus s-adenosyl-l-homocysteine2 hydrolase in complex with adenine
57d1li4a1
not modelled 97.7 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
58c1nytC_
not modelled 97.7 15 PDB header:oxidoreductase
Chain: C: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: shikimate dehydrogenase aroe complexed with nadp+
59d1gdha1
not modelled 97.7 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
60c3n7uD_
not modelled 97.7 22 PDB header:oxidoreductase
Chain: D: PDB Molecule:formate dehydrogenase;
PDBTitle: nad-dependent formate dehydrogenase from higher-plant arabidopsis2 thaliana in complex with nad and azide
61d1np3a2
not modelled 97.7 23 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
62c2o3jC_
not modelled 97.7 18 PDB header:oxidoreductase
Chain: C: PDB Molecule:udp-glucose 6-dehydrogenase;
PDBTitle: structure of caenorhabditis elegans udp-glucose dehydrogenase
63c2j6iC_
not modelled 97.7 16 PDB header:oxidoreductase
Chain: C: PDB Molecule:formate dehydrogenase;
PDBTitle: candida boidinii formate dehydrogenase (fdh) c-terminal2 mutant
64c2dbqA_
not modelled 97.7 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:glyoxylate reductase;
PDBTitle: crystal structure of glyoxylate reductase (ph0597) from pyrococcus2 horikoshii ot3, complexed with nadp (i41)
65d1vpda2
not modelled 97.6 23 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
66d1a4ia1
not modelled 97.6 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
67c3ojlA_
not modelled 97.6 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:cap5o;
PDBTitle: native structure of the udp-n-acetyl-mannosamine dehydrogenase cap5o2 from staphylococcus aureus
68c2g76A_
not modelled 97.6 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of human 3-phosphoglycerate dehydrogenase
69c3n58D_
not modelled 97.6 20 PDB header:hydrolase
Chain: D: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of s-adenosyl-l-homocysteine hydrolase from brucella2 melitensis in ternary complex with nad and adenosine, orthorhombic3 form
70d2dlda1
not modelled 97.6 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
71d1v8ba1
not modelled 97.6 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
72d1leha1
not modelled 97.6 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
73c1wwkA_
not modelled 97.6 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from pyrococcus2 horikoshii ot3
74c2eklA_
not modelled 97.6 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: structure of st1218 protein from sulfolobus tokodaii
75d1j4aa1
not modelled 97.6 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
76c2omeA_
not modelled 97.5 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:c-terminal-binding protein 2;
PDBTitle: crystal structure of human ctbp2 dehydrogenase complexed with nad(h)
77c2nacA_
not modelled 97.5 14 PDB header:oxidoreductase(aldehyde(d),nad+(a))
Chain: A: PDB Molecule:nad-dependent formate dehydrogenase;
PDBTitle: high resolution structures of holo and apo formate dehydrogenase
78d1l7da1
not modelled 97.5 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
79c2gcgB_
not modelled 97.5 23 PDB header:oxidoreductase
Chain: B: PDB Molecule:glyoxylate reductase/hydroxypyruvate reductase;
PDBTitle: ternary crystal structure of human glyoxylate2 reductase/hydroxypyruvate reductase
80d1c1da1
not modelled 97.5 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
81d2cvza2
not modelled 97.5 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
82d1bg6a2
not modelled 97.5 14 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
83c1yb4A_
not modelled 97.5 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:tartronic semialdehyde reductase;
PDBTitle: crystal structure of the tartronic semialdehyde reductase from2 salmonella typhimurium lt2
84d1mv8a2
not modelled 97.5 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
85d1p77a1
not modelled 97.5 14 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
86c1v8bA_
not modelled 97.5 20 PDB header:hydrolase
Chain: A: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of a hydrolase
87c3g0oA_
not modelled 97.5 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:3-hydroxyisobutyrate dehydrogenase;
PDBTitle: crystal structure of 3-hydroxyisobutyrate dehydrogenase2 (ygbj) from salmonella typhimurium
88c1vpdA_
not modelled 97.5 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:tartronate semialdehyde reductase;
PDBTitle: x-ray crystal structure of tartronate semialdehyde reductase2 [salmonella typhimurium lt2]
89d1ygya1
not modelled 97.5 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
90c1ygyA_
not modelled 97.5 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of d-3-phosphoglycerate dehydrogenase from2 mycobacterium tuberculosis
91c3prjB_
not modelled 97.5 17 PDB header:oxidoreductase
Chain: B: PDB Molecule:udp-glucose 6-dehydrogenase;
PDBTitle: role of packing defects in the evolution of allostery and induced fit2 in human udp-glucose dehydrogenase.
92d1b0aa1
not modelled 97.5 23 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
93c3pefA_
not modelled 97.4 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase, nad-binding;
PDBTitle: crystal structure of gamma-hydroxybutyrate dehydrogenase from2 geobacter metallireducens in complex with nadp+
94c1bg6A_
not modelled 97.4 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:n-(1-d-carboxylethyl)-l-norvaline dehydrogenase;
PDBTitle: crystal structure of the n-(1-d-carboxylethyl)-l-norvaline2 dehydrogenase from arthrobacter sp. strain 1c
95c3d64A_
not modelled 97.4 22 PDB header:hydrolase
Chain: A: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of s-adenosyl-l-homocysteine hydrolase from2 burkholderia pseudomallei
96d1f0ya2
not modelled 97.4 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
97c2f1kD_
not modelled 97.4 20 PDB header:oxidoreductase
Chain: D: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of synechocystis arogenate dehydrogenase
98d1uxja1
not modelled 97.4 23 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
99d1e5qa1
not modelled 97.4 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
100c1j4aA_
not modelled 97.4 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-lactate dehydrogenase;
PDBTitle: insights into domain closure, substrate specificity and2 catalysis of d-lactate dehydrogenase from lactobacillus3 bulgaricus
101c2uyyD_
not modelled 97.4 21 PDB header:cytokine
Chain: D: PDB Molecule:n-pac protein;
PDBTitle: structure of the cytokine-like nuclear factor n-pac
102d1qp8a1
not modelled 97.4 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
103c2pi1C_
not modelled 97.4 19 PDB header:oxidoreductase
Chain: C: PDB Molecule:d-lactate dehydrogenase;
PDBTitle: crystal structure of d-lactate dehydrogenase from aquifex2 aeolicus complexed with nad and lactic acid
104c3hn2A_
not modelled 97.4 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-dehydropantoate 2-reductase;
PDBTitle: crystal structure of 2-dehydropantoate 2-reductase from geobacter2 metallireducens gs-15
105c3gg9C_
not modelled 97.4 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:d-3-phosphoglycerate dehydrogenase oxidoreductase protein;
PDBTitle: crystal structure of putative d-3-phosphoglycerate dehydrogenase2 oxidoreductase from ralstonia solanacearum
106c3evtA_
not modelled 97.4 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from2 lactobacillus plantarum
107c1e5lA_
not modelled 97.4 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:saccharopine reductase;
PDBTitle: apo saccharopine reductase from magnaporthe grisea
108c3hg7A_
not modelled 97.4 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-isomer specific 2-hydroxyacid dehydrogenase family
PDBTitle: crystal structure of d-isomer specific 2-hydroxyacid dehydrogenase2 family protein from aeromonas salmonicida subsp. salmonicida a449
109c2eggA_
not modelled 97.3 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate 5-dehydrogenase (aroe) from2 geobacillus kaustophilus
110d1pjca1
not modelled 97.3 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
111c3o8qB_
not modelled 97.3 14 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase i alpha;
PDBTitle: 1.45 angstrom resolution crystal structure of shikimate 5-2 dehydrogenase (aroe) from vibrio cholerae
112c3bazA_
not modelled 97.3 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:hydroxyphenylpyruvate reductase;
PDBTitle: structure of hydroxyphenylpyruvate reductase from coleus blumei in2 complex with nadp+
113c2q3eH_
not modelled 97.3 15 PDB header:oxidoreductase
Chain: H: PDB Molecule:udp-glucose 6-dehydrogenase;
PDBTitle: structure of human udp-glucose dehydrogenase complexed with nadh and2 udp-glucose
114c2axqA_
not modelled 97.3 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:saccharopine dehydrogenase;
PDBTitle: apo histidine-tagged saccharopine dehydrogenase (l-glu2 forming) from saccharomyces cerevisiae
115c2d0iC_
not modelled 97.3 19 PDB header:oxidoreductase
Chain: C: PDB Molecule:dehydrogenase;
PDBTitle: crystal structure ph0520 protein from pyrococcus horikoshii ot3
116d2f1ka2
not modelled 97.3 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
117c2w2kB_
not modelled 97.3 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:d-mandelate dehydrogenase;
PDBTitle: crystal structure of the apo forms of rhodotorula graminis2 d-mandelate dehydrogenase at 1.8a.
118c3l6dB_
not modelled 97.3 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative oxidoreductase;
PDBTitle: crystal structure of putative oxidoreductase from pseudomonas putida2 kt2440
119c3gvxA_
not modelled 97.3 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:glycerate dehydrogenase related protein;
PDBTitle: crystal structure of glycerate dehydrogenase related2 protein from thermoplasma acidophilum
120c3pgjB_
not modelled 97.3 13 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate dehydrogenase;
PDBTitle: 2.49 angstrom resolution crystal structure of shikimate 5-2 dehydrogenase (aroe) from vibrio cholerae o1 biovar eltor str. n169613 in complex with shikimate

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