Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A6D5
DateThu Jan 5 11:02:53 GMT 2012
Unique Job ID93862a7a82db52a6

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1vi2B_
Top template information
PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase 2;
PDBTitle: crystal structure of shikimate-5-dehydrogenase with nad
Confidence and coverage
Confidence:100.0% Coverage: 98%
282 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  MDVTAKYELIGLMAYPIRHSLSPEMQNKALEKAGLPFTYMAFEVDNDSFPGAIEGLKALK
Secondary structure 


















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Disorder  ?????






















































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   .........70.........80.........90.........100.........110.........120
Sequence  MRGTGVSMPNKQLACEYVDELTPAAKLVGAINTIVNDDGYLRGYNTDGTGHIRAIKESGF
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   .........130.........140.........150.........160.........170.........180
Sequence  DIKGKTMVLLGAGGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVT
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   .........190.........200.........210.........220.........230.........240
Sequence  VTDLADQQAFAEALASADILTNGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTK
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   .........250.........260.........270.........280........
Sequence  LLQQAQQAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA
Secondary structure 












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Disorder 












































???
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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 1vi2 chain B

3D model

Region: 6 - 287
Aligned: 282
Modelled: 282
Confidence: 100.0%
Identity: 96%
PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase 2;
PDBTitle: crystal structure of shikimate-5-dehydrogenase with nad

Phyre2

PDB 3toz chain A

3D model

Region: 2 - 284
Aligned: 283
Modelled: 283
Confidence: 100.0%
Identity: 49%
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.

Phyre2

PDB 1nvt chain A

3D model

Region: 1 - 284
Aligned: 276
Modelled: 284
Confidence: 100.0%
Identity: 35%
PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate 5'-dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase (aroe or2 mj1084) in complex with nadp+

Phyre2

PDB 2hk8 chain B

3D model

Region: 3 - 284
Aligned: 263
Modelled: 268
Confidence: 100.0%
Identity: 35%
PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from aquifex2 aeolicus at 2.35 angstrom resolution

Phyre2

PDB 2egg chain A

3D model

Region: 5 - 284
Aligned: 270
Modelled: 280
Confidence: 100.0%
Identity: 34%
PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate 5-dehydrogenase (aroe) from2 geobacillus kaustophilus

Phyre2

PDB 3fbt chain B

3D model

Region: 6 - 285
Aligned: 257
Modelled: 258
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase, lyase
Chain: B: PDB Molecule:chorismate mutase and shikimate 5-dehydrogenase
PDBTitle: crystal structure of a chorismate mutase/shikimate 5-2 dehydrogenase fusion protein from clostridium3 acetobutylicum

Phyre2

PDB 1nyt chain C

3D model

Region: 8 - 284
Aligned: 263
Modelled: 267
Confidence: 100.0%
Identity: 27%
PDB header:oxidoreductase
Chain: C: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: shikimate dehydrogenase aroe complexed with nadp+

Phyre2

PDB 3pwz chain A

3D model

Region: 7 - 284
Aligned: 264
Modelled: 278
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase 3;
PDBTitle: crystal structure of an ael1 enzyme from pseudomonas putida

Phyre2

PDB 1npy chain A

3D model

Region: 3 - 286
Aligned: 263
Modelled: 268
Confidence: 100.0%
Identity: 30%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical shikimate 5-dehydrogenase-like
PDBTitle: structure of shikimate 5-dehydrogenase-like protein hi0607

Phyre2

PDB 2nlo chain A

3D model

Region: 6 - 284
Aligned: 272
Modelled: 279
Confidence: 100.0%
Identity: 25%
PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of the quinate dehydrogenase from corynebacterium2 glutamicum

Phyre2

PDB 3o8q chain B

3D model

Region: 8 - 284
Aligned: 259
Modelled: 277
Confidence: 100.0%
Identity: 30%
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

Phyre2

PDB 2o7q chain A

3D model

Region: 1 - 284
Aligned: 258
Modelled: 284
Confidence: 100.0%
Identity: 31%
PDB header:oxidoreductase,transferase
Chain: A: PDB Molecule:bifunctional 3-dehydroquinate dehydratase/shikimate
PDBTitle: crystal structure of the a. thaliana dhq-dehydroshikimate-sdh-2 shikimate-nadp(h)

Phyre2

PDB 2ev9 chain B

3D model

Region: 8 - 284
Aligned: 256
Modelled: 264
Confidence: 100.0%
Identity: 33%
PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate 5-dehydrogenase (aroe) from thermus2 thermophilus hb8 in complex with nadp(h) and shikimate

Phyre2

PDB 1p74 chain B

3D model

Region: 8 - 284
Aligned: 257
Modelled: 267
Confidence: 100.0%
Identity: 27%
PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase (aroe) from2 haemophilus influenzae

Phyre2

PDB 3pgj chain B

3D model

Region: 8 - 284
Aligned: 260
Modelled: 263
Confidence: 100.0%
Identity: 29%
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

Phyre2

PDB 3don chain A

3D model

Region: 10 - 284
Aligned: 252
Modelled: 252
Confidence: 100.0%
Identity: 31%
PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from staphylococcus2 epidermidis

Phyre2

PDB 3u62 chain A

3D model

Region: 10 - 284
Aligned: 247
Modelled: 258
Confidence: 100.0%
Identity: 29%
PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from thermotoga maritima

Phyre2

PDB 1vi2 chain A domain 1

3D model

Region: 107 - 288
Aligned: 182
Modelled: 182
Confidence: 100.0%
Identity: 97%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2

PDB 1nvt chain A domain 1

3D model

Region: 107 - 284
Aligned: 171
Modelled: 178
Confidence: 100.0%
Identity: 30%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Aminoacid dehydrogenase-like, C-terminal domain

Phyre2

PDB 1npy chain A domain 1

3D model

Region: 107 - 286
Aligned: 163
Modelled: 167
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
1

c1vi2B_
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c3tozA_
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c1nvtA_
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c2hk8B_
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c2eggA_
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c3fbtB_
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c1nytC_
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c3pwzA_
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c1npyA_
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c2nloA_
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c3o8qB_
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c2o7qA_
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c2ev9B_
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c1p74B_
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c3pgjB_
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c3donA_
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c3u62A_
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d1vi2a1
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d1nvta1
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d1npya1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1vi2B_



100.0 96 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase 2;
PDBTitle: crystal structure of shikimate-5-dehydrogenase with nad
2c3tozA_



100.0 49 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.
3c1nvtA_



100.0 35 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate 5'-dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase (aroe or2 mj1084) in complex with nadp+
4c2hk8B_



100.0 35 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from aquifex2 aeolicus at 2.35 angstrom resolution
5c2eggA_



100.0 34 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate 5-dehydrogenase (aroe) from2 geobacillus kaustophilus
6c3fbtB_



100.0 28 PDB header:oxidoreductase, lyase
Chain: B: PDB Molecule:chorismate mutase and shikimate 5-dehydrogenase
PDBTitle: crystal structure of a chorismate mutase/shikimate 5-2 dehydrogenase fusion protein from clostridium3 acetobutylicum
7c1nytC_



100.0 27 PDB header:oxidoreductase
Chain: C: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: shikimate dehydrogenase aroe complexed with nadp+
8c3pwzA_



100.0 28 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase 3;
PDBTitle: crystal structure of an ael1 enzyme from pseudomonas putida
9c1npyA_



100.0 30 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical shikimate 5-dehydrogenase-like
PDBTitle: structure of shikimate 5-dehydrogenase-like protein hi0607
10c2nloA_



100.0 25 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of the quinate dehydrogenase from corynebacterium2 glutamicum
11c3o8qB_



100.0 30 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
12c2o7qA_



100.0 31 PDB header:oxidoreductase,transferase
Chain: A: PDB Molecule:bifunctional 3-dehydroquinate dehydratase/shikimate
PDBTitle: crystal structure of the a. thaliana dhq-dehydroshikimate-sdh-2 shikimate-nadp(h)
13c2ev9B_



100.0 33 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate 5-dehydrogenase (aroe) from thermus2 thermophilus hb8 in complex with nadp(h) and shikimate
14c1p74B_



100.0 27 PDB header:oxidoreductase
Chain: B: PDB Molecule:shikimate 5-dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase (aroe) from2 haemophilus influenzae
15c3pgjB_



100.0 29 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
16c3donA_



100.0 31 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from staphylococcus2 epidermidis
17c3u62A_



100.0 29 PDB header:oxidoreductase
Chain: A: PDB Molecule:shikimate dehydrogenase;
PDBTitle: crystal structure of shikimate dehydrogenase from thermotoga maritima
18d1vi2a1



100.0 97 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
19d1nvta1



100.0 30 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
20d1npya1



100.0 25 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
21d1nyta1



not modelled 100.0 26 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
22d1vi2a2



not modelled 100.0 95 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Shikimate dehydrogenase-like
23d1nvta2



not modelled 100.0 42 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Shikimate dehydrogenase-like
24d1p77a1



not modelled 100.0 24 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
25d1p77a2



not modelled 100.0 32 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Shikimate dehydrogenase-like
26d1nyta2



not modelled 100.0 30 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Shikimate dehydrogenase-like
27d1npya2



not modelled 100.0 39 Fold:Aminoacid dehydrogenase-like, N-terminal domain
Superfamily:Aminoacid dehydrogenase-like, N-terminal domain
Family:Shikimate dehydrogenase-like
28c1luaA_



not modelled 100.0 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:methylene tetrahydromethanopterin dehydrogenase;
PDBTitle: structure of methylene-tetrahydromethanopterin dehydrogenase from2 methylobacterium extorquens am1 complexed with nadp
29d1luaa1



not modelled 99.5 30 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
30c1e5lA_



not modelled 99.2 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:saccharopine reductase;
PDBTitle: apo saccharopine reductase from magnaporthe grisea
31c2axqA_



not modelled 99.2 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:saccharopine dehydrogenase;
PDBTitle: apo histidine-tagged saccharopine dehydrogenase (l-glu2 forming) from saccharomyces cerevisiae
32c1gpjA_



not modelled 99.2 14 PDB header:reductase
Chain: A: PDB Molecule:glutamyl-trna reductase;
PDBTitle: glutamyl-trna reductase from methanopyrus kandleri
33c2rirA_



not modelled 99.0 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:dipicolinate synthase, a chain;
PDBTitle: crystal structure of dipicolinate synthase, a chain, from bacillus2 subtilis
34d1gpja2



not modelled 99.0 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
35c3d4oA_



not modelled 98.9 19 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
36c4a26B_



not modelled 98.9 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
37d1pjca1



not modelled 98.8 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
38c4a5oB_



not modelled 98.8 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of pseudomonas aeruginosa n5, n10-2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase (fold)
39c1a4iB_



not modelled 98.7 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase /
PDBTitle: human tetrahydrofolate dehydrogenase / cyclohydrolase
40d1b0aa1



not modelled 98.7 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
41c3l07B_



not modelled 98.6 19 PDB header:oxidoreductase,hydrolase
Chain: B: PDB Molecule:bifunctional protein fold;
PDBTitle: methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate2 cyclohydrolase, putative bifunctional protein fold from francisella3 tularensis.
42d1e5qa1



not modelled 98.6 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
43c3oj0A_



not modelled 98.6 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:glutamyl-trna reductase;
PDBTitle: crystal structure of glutamyl-trna reductase from thermoplasma2 volcanium (nucleotide binding domain)
44d1l7da1



not modelled 98.5 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
45d1a4ia1



not modelled 98.5 23 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
46c2z2vA_



not modelled 98.5 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:hypothetical protein ph1688;
PDBTitle: crystal structure of l-lysine dehydrogenase from2 hyperthermophilic archaeon pyrococcus horikoshii
47c3p2oB_



not modelled 98.4 16 PDB header:oxidoreductase, hydrolase
Chain: B: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of fold bifunctional protein from campylobacter2 jejuni
48d1x7da_



not modelled 98.4 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Ornithine cyclodeaminase-like
49c2i99A_



not modelled 98.4 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:mu-crystallin homolog;
PDBTitle: crystal structure of human mu_crystallin at 2.6 angstrom
50d1li4a1



not modelled 98.4 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
51c2eezG_



not modelled 98.3 15 PDB header:oxidoreductase
Chain: G: PDB Molecule:alanine dehydrogenase;
PDBTitle: crystal structure of alanine dehydrogenase from themus thermophilus
52c1b0aA_



not modelled 98.3 19 PDB header:oxidoreductase,hydrolase
Chain: A: PDB Molecule:protein (fold bifunctional protein);
PDBTitle: 5,10, methylene-tetrahydropholate2 dehydrogenase/cyclohydrolase from e coli.
53c3gvpB_



not modelled 98.3 13 PDB header:hydrolase
Chain: B: PDB Molecule:adenosylhomocysteinase 3;
PDBTitle: human sahh-like domain of human adenosylhomocysteinase 3
54c3p2oA_



not modelled 98.3 17 PDB header:oxidoreductase, hydrolase
Chain: A: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of fold bifunctional protein from campylobacter2 jejuni
55c1pjcA_



not modelled 98.3 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:protein (l-alanine dehydrogenase);
PDBTitle: l-alanine dehydrogenase complexed with nad
56c2bruB_



not modelled 98.1 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:nad(p) transhydrogenase subunit alpha;
PDBTitle: complex of the domain i and domain iii of escherichia coli2 transhydrogenase
57d1v8ba1



not modelled 98.1 14 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
58d1omoa_



not modelled 98.1 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Ornithine cyclodeaminase-like
59c3p2yA_



not modelled 98.1 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:alanine dehydrogenase/pyridine nucleotide transhydrogenase;
PDBTitle: crystal structure of alanine dehydrogenase/pyridine nucleotide2 transhydrogenase from mycobacterium smegmatis
60c2a9fB_



not modelled 98.0 17 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))
61c3ic5A_



not modelled 98.0 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative saccharopine dehydrogenase;
PDBTitle: n-terminal domain of putative saccharopine dehydrogenase from ruegeria2 pomeroyi.
62c3nglA_



not modelled 98.0 16 PDB header:oxidoreductase, hydrolase
Chain: A: PDB Molecule:bifunctional protein fold;
PDBTitle: crystal structure of bifunctional 5,10-methylenetetrahydrofolate2 dehydrogenase / cyclohydrolase from thermoplasma acidophilum
63c2vhyB_



not modelled 97.9 17 PDB header:oxidoreductase
Chain: B: PDB Molecule:alanine dehydrogenase;
PDBTitle: crystal structure of apo l-alanine dehydrogenase from2 mycobacterium tuberculosis
64d1c1da1



not modelled 97.9 11 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
65c1d4fD_



not modelled 97.9 17 PDB header:hydrolase
Chain: D: PDB Molecule:s-adenosylhomocysteine hydrolase;
PDBTitle: crystal structure of recombinant rat-liver d244e mutant s-2 adenosylhomocysteine hydrolase
66d1bg6a2



not modelled 97.9 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
67c2ph5A_



not modelled 97.9 16 PDB header:transferase
Chain: A: PDB Molecule:homospermidine synthase;
PDBTitle: crystal structure of the homospermidine synthase hss from legionella2 pneumophila in complex with nad, northeast structural genomics target3 lgr54
68d2pgda2



not modelled 97.9 14 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
69c3n58D_



not modelled 97.8 17 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
70c2g5cD_



not modelled 97.8 16 PDB header:oxidoreductase
Chain: D: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from aquifex aeolicus
71c1l7eC_



not modelled 97.8 14 PDB header:oxidoreductase
Chain: C: PDB Molecule:nicotinamide nucleotide transhydrogenase,
PDBTitle: crystal structure of r. rubrum transhydrogenase domain i2 with bound nadh
72c3gucB_



not modelled 97.8 14 PDB header:transferase
Chain: B: PDB Molecule:ubiquitin-like modifier-activating enzyme 5;
PDBTitle: human ubiquitin-activating enzyme 5 in complex with amppnp
73d1uxja1



not modelled 97.8 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
74d1pzga1



not modelled 97.8 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
75c2c2xB_



not modelled 97.8 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase-
PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis
76d2naca1



not modelled 97.7 12 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
77c3dhyC_



not modelled 97.7 17 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
78c1bg6A_



not modelled 97.7 17 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
79d1leha1



not modelled 97.7 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
80c3fwnB_



not modelled 97.7 14 PDB header:oxidoreductase
Chain: B: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating;
PDBTitle: dimeric 6-phosphogluconate dehydrogenase complexed with 6-2 phosphogluconate and 2'-monophosphoadenosine-5'-diphosphate
81c2f1kD_



not modelled 97.7 20 PDB header:oxidoreductase
Chain: D: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of synechocystis arogenate dehydrogenase
82d2jfga1



not modelled 97.7 21 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
83c3ktdC_



not modelled 97.7 14 PDB header:oxidoreductase
Chain: C: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of a putative prephenate dehydrogenase (cgl0226)2 from corynebacterium glutamicum atcc 13032 at 2.60 a resolution
84c1np3B_



not modelled 97.6 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:ketol-acid reductoisomerase;
PDBTitle: crystal structure of class i acetohydroxy acid isomeroreductase from2 pseudomonas aeruginosa
85c3dfzB_



not modelled 97.6 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:precorrin-2 dehydrogenase;
PDBTitle: sirc, precorrin-2 dehydrogenase
86d1jw9b_



not modelled 97.6 22 Fold:Activating enzymes of the ubiquitin-like proteins
Superfamily:Activating enzymes of the ubiquitin-like proteins
Family:Molybdenum cofactor biosynthesis protein MoeB
87c3kydB_



not modelled 97.6 15 PDB header:ligase
Chain: B: PDB Molecule:sumo-activating enzyme subunit 2;
PDBTitle: human sumo e1~sumo1-amp tetrahedral intermediate mimic
88c1v8bA_



not modelled 97.6 18 PDB header:hydrolase
Chain: A: PDB Molecule:adenosylhomocysteinase;
PDBTitle: crystal structure of a hydrolase
89c1pgqA_



not modelled 97.6 13 PDB header:oxidoreductase (choh(d)-nadp+(a))
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase;
PDBTitle: crystallographic study of coenzyme, coenzyme analogue and substrate2 binding in 6-phosphogluconate dehydrogenase: implications for nadp3 specificity and the enzyme mechanism
90c3k96B_



not modelled 97.6 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:glycerol-3-phosphate dehydrogenase [nad(p)+];
PDBTitle: 2.1 angstrom resolution crystal structure of glycerol-3-phosphate2 dehydrogenase (gpsa) from coxiella burnetii
91c1y8qD_



not modelled 97.6 16 PDB header:ligase
Chain: D: PDB Molecule:ubiquitin-like 2 activating enzyme e1b;
PDBTitle: sumo e1 activating enzyme sae1-sae2-mg-atp complex
92c1pgjA_



not modelled 97.6 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase;
PDBTitle: x-ray structure of 6-phosphogluconate dehydrogenase from the protozoan2 parasite t. brucei
93c2ew2B_



not modelled 97.6 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:2-dehydropantoate 2-reductase, putative;
PDBTitle: crystal structure of the putative 2-dehydropantoate 2-reductase from2 enterococcus faecalis
94c2hjrK_



not modelled 97.6 15 PDB header:oxidoreductase
Chain: K: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of cryptosporidium parvum malate2 dehydrogenase
95c1wwkA_



not modelled 97.6 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from pyrococcus2 horikoshii ot3
96c3vh3A_



not modelled 97.6 22 PDB header:metal binding protein/protein transport
Chain: A: PDB Molecule:ubiquitin-like modifier-activating enzyme atg7;
PDBTitle: crystal structure of atg7ctd-atg8 complex
97c3triB_



not modelled 97.6 14 PDB header:oxidoreductase
Chain: B: PDB Molecule:pyrroline-5-carboxylate reductase;
PDBTitle: structure of a pyrroline-5-carboxylate reductase (proc) from coxiella2 burnetii
98d1yovb1



not modelled 97.6 20 Fold:Activating enzymes of the ubiquitin-like proteins
Superfamily:Activating enzymes of the ubiquitin-like proteins
Family:Ubiquitin activating enzymes (UBA)
99c3h9gA_



not modelled 97.6 22 PDB header:transferase/antibiotic
Chain: A: PDB Molecule:mccb protein;
PDBTitle: crystal structure of e. coli mccb + mcca-n7isoasn
100c3d1lB_



not modelled 97.6 25 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative nadp oxidoreductase bf3122;
PDBTitle: crystal structure of putative nadp oxidoreductase bf3122 from2 bacteroides fragilis
101d1ygya1



not modelled 97.6 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
102c2fnzA_



not modelled 97.6 11 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)
103c2g76A_



not modelled 97.5 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of human 3-phosphoglycerate dehydrogenase
104c1edzA_



not modelled 97.5 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:5,10-methylenetetrahydrofolate dehydrogenase;
PDBTitle: structure of the nad-dependent 5,10-2 methylenetetrahydrofolate dehydrogenase from saccharomyces3 cerevisiae
105c3hdjA_



not modelled 97.5 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:probable ornithine cyclodeaminase;
PDBTitle: the crystal structure of probable ornithine cyclodeaminase from2 bordetella pertussis tohama i
106c3oneA_



not modelled 97.5 14 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
107c2p4qA_



not modelled 97.5 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating 1;
PDBTitle: crystal structure analysis of gnd1 in saccharomyces cerevisiae
108c3hg7A_



not modelled 97.5 19 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
109c3gznB_



not modelled 97.5 20 PDB header:protein binding/ligase
Chain: B: PDB Molecule:nedd8-activating enzyme e1 catalytic subunit;
PDBTitle: structure of nedd8-activating enzyme in complex with nedd82 and mln4924
110c2iz1C_



not modelled 97.5 12 PDB header:oxidoreductase
Chain: C: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating;
PDBTitle: 6pdh complexed with pex inhibitor synchrotron data
111c1pzfD_



not modelled 97.5 19 PDB header:oxidoreductase
Chain: D: PDB Molecule:lactate dehydrogenase;
PDBTitle: t.gondii ldh1 ternary complex with apad+ and oxalate
112c1z82A_



not modelled 97.5 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:glycerol-3-phosphate dehydrogenase;
PDBTitle: crystal structure of glycerol-3-phosphate dehydrogenase (tm0378) from2 thermotoga maritima at 2.00 a resolution
113d1i0za1



not modelled 97.5 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
114c3c24A_



not modelled 97.5 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:putative oxidoreductase;
PDBTitle: crystal structure of a putative oxidoreductase (yp_511008.1) from2 jannaschia sp. ccs1 at 1.62 a resolution
115c3vh1A_



not modelled 97.5 22 PDB header:metal binding protein
Chain: A: PDB Molecule:ubiquitin-like modifier-activating enzyme atg7;
PDBTitle: crystal structure of saccharomyces cerevisiae atg7 (1-595)
116c3b1fA_



not modelled 97.5 23 PDB header:oxidoreductase
Chain: A: PDB Molecule:putative prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from streptococcus2 mutans
117d9ldta1



not modelled 97.5 12 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
118c1m75B_



not modelled 97.5 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:3-hydroxyacyl-coa dehydrogenase;
PDBTitle: crystal structure of the n208s mutant of l-3-hydroxyacyl-2 coa dehydrogenase in complex with nad and acetoacetyl-coa
119c1zfnA_



not modelled 97.5 22 PDB header:transferase
Chain: A: PDB Molecule:adenylyltransferase thif;
PDBTitle: structural analysis of escherichia coli thif
120d1txga2



not modelled 97.5 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain

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