Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76558
DateThu Jan 5 12:24:36 GMT 2012
Unique Job ID3e1b2ff60c958c08

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1ww8A_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:malate oxidoreductase;
PDBTitle: crystal structure of malic enzyme from pyrococcus2 horikoshii ot3
Confidence and coverage
Confidence:100.0% Coverage: 53%
404 residues ( 53% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
738 residues ( 97%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MDDQLKQSALDFHEFPVPGKIQVSPTKPLATQRDLALAYSPGVAAPCLEIEKDPLKAYKY
Secondary structure 
SS confidence 
Disorder  ??
?
???
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  TARGNLVAVISNGTAVLGLGNIGALAGKPVMEGKGVLFKKFAGIDVFDIEVDELDPDKFI
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  EVVAALEPTFGGINLEDIKAPECFYIEQKLRERMNIPVFHDDQHGTAIISTAAILNGLRV
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  VEKNISDVRMVVSGAGAAAIACMNLLVALGLQKHNIVVCDSKGVIYQGREPNMAETKAAY
Secondary structure 
SS confidence 
Disorder  ???
?????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  AVVDDGKRTLDDVIEGADIFLGCSGPKVLTQEMVKKMARAPMILALANPEPEILPPLAKE
Secondary structure 
SS confidence 
Disorder 
??????
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  VRPDAIICTGRSDYPNQVNNVLCFPFIFRGALDVGATAINEEMKLAAVRAIAELAHAEQS
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  EVVASAYGDQDLSFGPEYIIPKPFDPRLIVKIAPAVAKAAMESGVATRPIADFDVYIDKL
Secondary structure 
SS confidence 
Disorder 
?????
??
??
???????????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  TEFVYKTNLFMKPIFSQARKAPKRVVLPEGEEARVLHATQELVTLGLAKPILIGRPNVIE
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  MRIQKLGLQIKAGVDFEIVNNESDPRFKEYWTEYFQIMKRRGVTQEQAQRALISNPTVIG
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  AIMVQRGEADAMICGTVGDYHEHFSVVKNVFGYRDGVHTAGAMNALLLPSGNTFIADTYV
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  NDEPDAEELAEITLMAAETVRRFGIEPRVALLSHSNFGSSDCPSSSKMRQALELVRERAP
Secondary structure 
SS confidence 
Disorder 
?????????
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  ELMIDGEMHGDAALVEAIRNDRMPDSSLKGSANILVMPNMEAARISYNLLRVSSSEGVTV
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........730.........740.........750.........
Sequence  GPVLMGVAKPVHVLTPIASVRRIVNMVALAVVEAQTQPL
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 1ww8 chain A

3D model

Region: 5 - 426
Aligned: 404
Modelled: 401
Confidence: 100.0%
Identity: 45%
PDB header:oxidoreductase
Chain: A: PDB Molecule:malate oxidoreductase;
PDBTitle: crystal structure of malic enzyme from pyrococcus2 horikoshii ot3

Phyre2

PDB 2a9f chain B

3D model

Region: 1 - 396
Aligned: 378
Modelled: 382
Confidence: 100.0%
Identity: 48%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative malic enzyme ((s)-malate:nad+
PDBTitle: crystal structure of a putative malic enzyme ((s)-2 malate:nad+ oxidoreductase (decarboxylating))

Phyre2

PDB 3nv9 chain A

3D model

Region: 5 - 436
Aligned: 416
Modelled: 418
Confidence: 100.0%
Identity: 38%
PDB header:oxidoreductase
Chain: A: PDB Molecule:malic enzyme;
PDBTitle: crystal structure of entamoeba histolytica malic enzyme

Phyre2

PDB 1vl6 chain C

3D model

Region: 8 - 400
Aligned: 371
Modelled: 376
Confidence: 100.0%
Identity: 47%
PDB header:oxidoreductase
Chain: C: PDB Molecule:malate oxidoreductase;
PDBTitle: crystal structure of nad-dependent malic enzyme (tm0542) from2 thermotoga maritima at 2.61 a resolution

Phyre2

PDB 1gz3 chain B

3D model

Region: 33 - 420
Aligned: 371
Modelled: 374
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase
Chain: B: PDB Molecule:nad-dependent malic enzyme;
PDBTitle: molecular mechanism for the regulation of human mitochondrial2 nad(p)+-dependent malic enzyme by atp and fumarate

Phyre2

PDB 1qr6 chain A

3D model

Region: 33 - 419
Aligned: 370
Modelled: 370
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase
Chain: A: PDB Molecule:malic enzyme 2;
PDBTitle: human mitochondrial nad(p)-dependent malic enzyme

Phyre2

PDB 2aw5 chain A

3D model

Region: 35 - 419
Aligned: 362
Modelled: 370
Confidence: 100.0%
Identity: 30%
PDB header:oxidoreductase
Chain: A: PDB Molecule:nadp-dependent malic enzyme;
PDBTitle: crystal structure of a human malic enzyme

Phyre2

PDB 1o0s chain B

3D model

Region: 33 - 420
Aligned: 370
Modelled: 373
Confidence: 100.0%
Identity: 27%
PDB header:oxidoreductase
Chain: B: PDB Molecule:nad-dependent malic enzyme;
PDBTitle: crystal structure of ascaris suum malic enzyme complexed with nadh

Phyre2

PDB 1vmi chain A

3D model

Region: 428 - 752
Aligned: 319
Modelled: 325
Confidence: 100.0%
Identity: 33%
PDB header:transferase
Chain: A: PDB Molecule:putative phosphate acetyltransferase;
PDBTitle: crystal structure of putative phosphate acetyltransferase2 (np_416953.1) from escherichia coli k12 at 2.32 a resolution

Phyre2

PDB 1vmi chain A

3D model

Region: 428 - 752
Aligned: 319
Modelled: 325
Confidence: 100.0%
Identity: 33%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Phosphotransacetylase

Phyre2

PDB 1xco chain A

3D model

Region: 428 - 754
Aligned: 321
Modelled: 327
Confidence: 100.0%
Identity: 29%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Phosphotransacetylase

Phyre2

PDB 1r5j chain A

3D model

Region: 427 - 754
Aligned: 322
Modelled: 328
Confidence: 100.0%
Identity: 28%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Phosphotransacetylase

Phyre2

PDB 2af4 chain C domain 1

3D model

Region: 429 - 757
Aligned: 322
Modelled: 329
Confidence: 100.0%
Identity: 29%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Phosphotransacetylase

Phyre2

PDB 1o0s chain A domain 1

3D model

Region: 163 - 420
Aligned: 243
Modelled: 244
Confidence: 100.0%
Identity: 26%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2

PDB 1gq2 chain A domain 1

3D model

Region: 163 - 419
Aligned: 242
Modelled: 243
Confidence: 100.0%
Identity: 29%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2

PDB 1pj3 chain A domain 1

3D model

Region: 163 - 419
Aligned: 243
Modelled: 243
Confidence: 100.0%
Identity: 25%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2

PDB 1vl6 chain A domain 1

3D model

Region: 162 - 400
Aligned: 218
Modelled: 222
Confidence: 100.0%
Identity: 43%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2

PDB 3tng chain A

3D model

Region: 438 - 755
Aligned: 274
Modelled: 289
Confidence: 100.0%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:lmo1369 protein;
PDBTitle: the crystal structure of a possible phosphate acetyl/butaryl2 transferase from listeria monocytogenes egd-e.

Phyre2

PDB 1yco chain A

3D model

Region: 444 - 755
Aligned: 268
Modelled: 283
Confidence: 100.0%
Identity: 19%
PDB header:transferase
Chain: A: PDB Molecule:branched-chain phosphotransacylase;
PDBTitle: crystal structure of a branched-chain phosphotransacylase from2 enterococcus faecalis v583

Phyre2

PDB 1vl6 chain A domain 2

3D model

Region: 8 - 161
Aligned: 153
Modelled: 154
Confidence: 100.0%
Identity: 53%
Fold: Aminoacid dehydrogenase-like, N-terminal domain
Superfamily: Aminoacid dehydrogenase-like, N-terminal domain
Family: Malic enzyme N-domain

Phyre2
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c1ww8A_
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c2a9fB_
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c3nv9A_
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c1vl6C_
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c1gz3B_
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c1qr6A_
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c2aw5A_
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c1o0sB_
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c1vmiA_
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d1vmia_
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d1xcoa_
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d2af4c1
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d1o0sa1
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d1gq2a1
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c3tngA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1ww8A_
100.0 45 PDB header:oxidoreductase
Chain: A: PDB Molecule:malate oxidoreductase;
PDBTitle: crystal structure of malic enzyme from pyrococcus2 horikoshii ot3
2c2a9fB_
100.0 48 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative malic enzyme ((s)-malate:nad+
PDBTitle: crystal structure of a putative malic enzyme ((s)-2 malate:nad+ oxidoreductase (decarboxylating))
3c3nv9A_
100.0 38 PDB header:oxidoreductase
Chain: A: PDB Molecule:malic enzyme;
PDBTitle: crystal structure of entamoeba histolytica malic enzyme
4c1vl6C_
100.0 47 PDB header:oxidoreductase
Chain: C: PDB Molecule:malate oxidoreductase;
PDBTitle: crystal structure of nad-dependent malic enzyme (tm0542) from2 thermotoga maritima at 2.61 a resolution
5c1gz3B_
100.0 28 PDB header:oxidoreductase
Chain: B: PDB Molecule:nad-dependent malic enzyme;
PDBTitle: molecular mechanism for the regulation of human mitochondrial2 nad(p)+-dependent malic enzyme by atp and fumarate
6c1qr6A_
100.0 28 PDB header:oxidoreductase
Chain: A: PDB Molecule:malic enzyme 2;
PDBTitle: human mitochondrial nad(p)-dependent malic enzyme
7c2aw5A_
100.0 30 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadp-dependent malic enzyme;
PDBTitle: crystal structure of a human malic enzyme
8c1o0sB_
100.0 27 PDB header:oxidoreductase
Chain: B: PDB Molecule:nad-dependent malic enzyme;
PDBTitle: crystal structure of ascaris suum malic enzyme complexed with nadh
9c1vmiA_
100.0 33 PDB header:transferase
Chain: A: PDB Molecule:putative phosphate acetyltransferase;
PDBTitle: crystal structure of putative phosphate acetyltransferase2 (np_416953.1) from escherichia coli k12 at 2.32 a resolution
10d1vmia_
100.0 33 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Phosphotransacetylase
11d1xcoa_
100.0 29 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Phosphotransacetylase
12d1r5ja_
100.0 28 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Phosphotransacetylase
13d2af4c1
100.0 29 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Phosphotransacetylase
14d1o0sa1
100.0 26 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
15d1gq2a1
100.0 29 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
16d1pj3a1
100.0 25 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
17d1vl6a1
100.0 43 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
18c3tngA_
100.0 20 PDB header:transferase
Chain: A: PDB Molecule:lmo1369 protein;
PDBTitle: the crystal structure of a possible phosphate acetyl/butaryl2 transferase from listeria monocytogenes egd-e.
19c1ycoA_
100.0 19 PDB header:transferase
Chain: A: PDB Molecule:branched-chain phosphotransacylase;
PDBTitle: crystal structure of a branched-chain phosphotransacylase from2 enterococcus faecalis v583
20d1vl6a2
100.0 53 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Malic enzyme N-domain
21d1pj3a2
not modelled 100.0 32 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Malic enzyme N-domain
22d1gq2a2
not modelled 100.0 31 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Malic enzyme N-domain
23d1vi1a_
not modelled 100.0 18 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:PlsX-like
24d1o0sa2
not modelled 100.0 27 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Malic enzyme N-domain
25d1u7na_
not modelled 100.0 23 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:PlsX-like
26d1ptma_
not modelled 99.8 18 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:PdxA-like
27c1yxoB_
not modelled 99.6 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:4-hydroxythreonine-4-phosphate dehydrogenase 1;
PDBTitle: crystal structure of pyridoxal phosphate biosynthetic protein pdxa2 pa0593
28d1r8ka_
not modelled 99.4 17 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:PdxA-like
29d1euza1
not modelled 98.9 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
30d1li4a1
not modelled 98.6 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
31c2hi1A_
not modelled 98.5 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:4-hydroxythreonine-4-phosphate dehydrogenase 2;
PDBTitle: the structure of a putative 4-hydroxythreonine-4-phosphate2 dehydrogenase from salmonella typhimurium.
32d1v9la1
not modelled 98.5 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
33c3tozA_
not modelled 98.4 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: 2.2 angstrom crystal structure of shikimate 5-dehydrogenase from2 listeria monocytogenes in complex with nad.
34c3d4oA_
not modelled 98.2 15 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
35c2rirA_
not modelled 98.1 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:dipicolinate synthase, a chain;
PDBTitle: crystal structure of dipicolinate synthase, a chain, from bacillus2 subtilis
36d1v8ba1
not modelled 98.1 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
37c3dhyC_
not modelled 98.0 18 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
38c3gvpB_
not modelled 98.0 21 PDB header:hydrolase
Chain: B: PDB Molecule:adenosylhomocysteinase 3;
PDBTitle: human sahh-like domain of human adenosylhomocysteinase 3
39c3n58D_
not modelled 97.9 22 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
40c3aoeC_
not modelled 97.9 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:glutamate dehydrogenase;
PDBTitle: crystal structure of hetero-hexameric glutamate dehydrogenase from2 thermus thermophilus (leu bound form)
41c1v8bA_
not modelled 97.9 17 PDB header:hydrolase
Chain: A: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of a hydrolase
42c1d4fD_
not modelled 97.9 18 PDB header:hydrolase
Chain: D: PDB Molecule:s-adenosylhomocysteine hydrolase;
PDBTitle: crystal structure of recombinant rat-liver d244e mutant s-2 adenosylhomocysteine hydrolase
43c3d64A_
not modelled 97.9 24 PDB header:hydrolase
Chain: A: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of s-adenosyl-l-homocysteine hydrolase from2 burkholderia pseudomallei
44c3oneA_
not modelled 97.8 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
45d1bvua1
not modelled 97.8 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
46d1vi2a1
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
47c3aogA_
not modelled 97.7 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase;
PDBTitle: crystal structure of glutamate dehydrogenase (gdhb) from thermus2 thermophilus (glu bound form)
48d1l7da1
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
49c1gpjA_
not modelled 97.7 21 PDB header:reductase
Chain: A: PDB Molecule:glutamyl-trna reductase;
PDBTitle: glutamyl-trna reductase from methanopyrus kandleri
50c1v9lA_
not modelled 97.6 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase;
PDBTitle: l-glutamate dehydrogenase from pyrobaculum islandicum2 complexed with nad
51d1b26a1
not modelled 97.6 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
52d1gpja2
not modelled 97.6 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
53c2bmaA_
not modelled 97.5 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase (nadp+);
PDBTitle: the crystal structure of plasmodium falciparum glutamate2 dehydrogenase, a putative target for novel antimalarial3 drugs
54d1gtma1
not modelled 97.5 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
55c3k8zD_
not modelled 97.5 18 PDB header:oxidoreductase
Chain: D: PDB Molecule:nad-specific glutamate dehydrogenase;
PDBTitle: crystal structure of gudb1 a decryptified secondary glutamate2 dehydrogenase from b. subtilis
56c1bvuF_
not modelled 97.4 18 PDB header:oxidoreductase
Chain: F: PDB Molecule:protein (glutamate dehydrogenase);
PDBTitle: glutamate dehydrogenase from thermococcus litoralis
57d1t2da1
not modelled 97.3 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
58d1hwxa1
not modelled 97.3 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
59d1bgva1
not modelled 97.2 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
60c1j4aA_
not modelled 97.2 20 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
61c2tmgD_
not modelled 97.2 17 PDB header:oxidoreductase
Chain: D: PDB Molecule:protein (glutamate dehydrogenase);
PDBTitle: thermotoga maritima glutamate dehydrogenase mutant s128r,2 t158e, n117r, s160e
62c3l07B_
not modelled 97.2 21 PDB header:oxidoreductase,hydrolase
Chain: B: PDB Molecule:bifunctional protein fold;
PDBTitle: methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate2 cyclohydrolase, putative bifunctional protein fold from francisella3 tularensis.
63d1pjca1
not modelled 97.1 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
64c2eklA_
not modelled 97.1 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: structure of st1218 protein from sulfolobus tokodaii
65c2j6iC_
not modelled 97.0 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:formate dehydrogenase;
PDBTitle: candida boidinii formate dehydrogenase (fdh) c-terminal2 mutant
66c3p2yA_
not modelled 96.9 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:alanine dehydrogenase/pyridine nucleotide transhydrogenase;
PDBTitle: crystal structure of alanine dehydrogenase/pyridine nucleotide2 transhydrogenase from mycobacterium smegmatis
67d1ygya1
not modelled 96.9 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
68d1nyta1
not modelled 96.9 11 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
69c2eezG_
not modelled 96.9 19 PDB header:oxidoreductase
Chain: G: PDB Molecule:alanine dehydrogenase;
PDBTitle: crystal structure of alanine dehydrogenase from themus thermophilus
70c1wwkA_
not modelled 96.9 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from pyrococcus2 horikoshii ot3
71d1uxja1
not modelled 96.9 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
72d1a4ia1
not modelled 96.8 24 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
73c1bxgA_
not modelled 96.8 20 PDB header:amino acid dehydrogenase
Chain: A: PDB Molecule:phenylalanine dehydrogenase;
PDBTitle: phenylalanine dehydrogenase structure in ternary complex2 with nad+ and beta-phenylpropionate
74d1gdha1
not modelled 96.8 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
75c3o8qB_
not modelled 96.8 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
76c1pjcA_
not modelled 96.8 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:protein (l-alanine dehydrogenase);
PDBTitle: l-alanine dehydrogenase complexed with nad
77c4a5oB_
not modelled 96.7 19 PDB header:oxidoreductase
Chain: B: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of pseudomonas aeruginosa n5, n10-2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase (fold)
78c3donA_
not modelled 96.7 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from staphylococcus2 epidermidis
79c1a4iB_
not modelled 96.7 24 PDB header:oxidoreductase
Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase /
PDBTitle: human tetrahydrofolate dehydrogenase / cyclohydrolase
80c3pgjB_
not modelled 96.7 15 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
81c2dbqA_
not modelled 96.6 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:glyoxylate reductase;
PDBTitle: crystal structure of glyoxylate reductase (ph0597) from pyrococcus2 horikoshii ot3, complexed with nadp (i41)
82c3evtA_
not modelled 96.6 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from2 lactobacillus plantarum
83d1b0aa1
not modelled 96.6 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
84c1p74B_
not modelled 96.6 13 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase (aroe) from2 haemophilus influenzae
85c3p2oB_
not modelled 96.6 19 PDB header:oxidoreductase, hydrolase
Chain: B: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of fold bifunctional protein from campylobacter2 jejuni
86c1hrdA_
not modelled 96.6 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase;
PDBTitle: glutamate dehydrogenase
87d1llda1
not modelled 96.6 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
88c2cukC_
not modelled 96.5 22 PDB header:oxidoreductase
Chain: C: PDB Molecule:glycerate dehydrogenase/glyoxylate reductase;
PDBTitle: crystal structure of tt0316 protein from thermus thermophilus hb8
89c3p2oA_
not modelled 96.5 19 PDB header:oxidoreductase, hydrolase
Chain: A: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of fold bifunctional protein from campylobacter2 jejuni
90d1pzga1
not modelled 96.5 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
91c1gdhA_
not modelled 96.5 19 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
92c4a26B_
not modelled 96.4 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative c-1-tetrahydrofolate synthase, cytoplasmic;
PDBTitle: the crystal structure of leishmania major n5,n10-2 methylenetetrahydrofolate dehydrogenase/cyclohydrolase
93d2naca1
not modelled 96.4 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
94c2d0iC_
not modelled 96.4 20 PDB header:oxidoreductase
Chain: C: PDB Molecule:dehydrogenase;
PDBTitle: crystal structure ph0520 protein from pyrococcus horikoshii ot3
95d1mx3a1
not modelled 96.4 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
96c2gcgB_
not modelled 96.4 13 PDB header:oxidoreductase
Chain: B: PDB Molecule:glyoxylate reductase/hydroxypyruvate reductase;
PDBTitle: ternary crystal structure of human glyoxylate2 reductase/hydroxypyruvate reductase
97c2yfqA_
not modelled 96.3 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:nad-specific glutamate dehydrogenase;
PDBTitle: crystal structure of glutamate dehydrogenase from2 peptoniphilus asaccharolyticus
98d1ez4a1
not modelled 96.3 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
99c3u62A_
not modelled 96.3 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from thermotoga maritima
100d1leha1
not modelled 96.3 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
101c1pzfD_
not modelled 96.3 16 PDB header:oxidoreductase
Chain: D: PDB Molecule:lactate dehydrogenase;
PDBTitle: t.gondii ldh1 ternary complex with apad+ and oxalate
102c1lehB_
not modelled 96.2 25 PDB header:oxidoreductase
Chain: B: PDB Molecule:leucine dehydrogenase;
PDBTitle: leucine dehydrogenase from bacillus sphaericus
103c3kboB_
not modelled 96.2 14 PDB header:oxidoreductase
Chain: B: PDB Molecule:glyoxylate/hydroxypyruvate reductase a;
PDBTitle: 2.14 angstrom crystal structure of putative oxidoreductase (ycdw) from2 salmonella typhimurium in complex with nadp
104c3hg7A_
not modelled 96.2 11 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
105c1l7eC_
not modelled 96.1 22 PDB header:oxidoreductase
Chain: C: PDB Molecule:nicotinamide nucleotide transhydrogenase,
PDBTitle: crystal structure of r. rubrum transhydrogenase domain i2 with bound nadh
106c3oj0A_
not modelled 96.1 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamyl-trna reductase;
PDBTitle: crystal structure of glutamyl-trna reductase from thermoplasma2 volcanium (nucleotide binding domain)
107c1b0aA_
not modelled 96.1 17 PDB header:oxidoreductase,hydrolase
Chain: A: PDB Molecule:protein (fold bifunctional protein);
PDBTitle: 5,10, methylene-tetrahydropholate2 dehydrogenase/cyclohydrolase from e coli.
108c3fefB_
not modelled 96.1 21 PDB header:hydrolase
Chain: B: PDB Molecule:putative glucosidase lpld;
PDBTitle: crystal structure of putative glucosidase lpld from2 bacillus subtilis
109d1u8xx1
not modelled 96.1 13 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
110d1qp8a1
not modelled 96.0 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
111c2g76A_
not modelled 96.0 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of human 3-phosphoglycerate dehydrogenase
112c1vi2B_
not modelled 96.0 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase 2;
PDBTitle: crystal structure of shikimate-5-dehydrogenase with nad
113c1xdwA_
not modelled 96.0 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:nad+-dependent (r)-2-hydroxyglutarate
PDBTitle: nad+-dependent (r)-2-hydroxyglutarate dehydrogenase from2 acidaminococcus fermentans
114c2fnzA_
not modelled 96.0 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:lactate dehydrogenase;
PDBTitle: crystal structure of the lactate dehydrogenase from cryptosporidium2 parvum complexed with cofactor (b-nicotinamide adenine dinucleotide)3 and inhibitor (oxamic acid)
115c1nr1A_
not modelled 96.0 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamate dehydrogenase 1;
PDBTitle: crystal structure of the r463a mutant of human glutamate2 dehydrogenase
116c1ur5C_
not modelled 95.9 20 PDB header:oxidoreductase
Chain: C: PDB Molecule:malate dehydrogenase;
PDBTitle: stabilization of a tetrameric malate dehydrogenase by2 introduction of a disulfide bridge at the dimer/dimer3 interface
117c3oetF_
not modelled 95.9 18 PDB header:oxidoreductase
Chain: F: PDB Molecule:erythronate-4-phosphate dehydrogenase;
PDBTitle: d-erythronate-4-phosphate dehydrogenase complexed with nad
118c2o4cB_
not modelled 95.8 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:erythronate-4-phosphate dehydrogenase;
PDBTitle: crystal structure of d-erythronate-4-phosphate dehydrogenase complexed2 with nad
119d9ldta1
not modelled 95.8 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
120c3n7uD_
not modelled 95.7 16 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

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