Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP37005
DateThu Jan 5 11:54:16 GMT 2012
Unique Job ID14a50a95ece1fa63

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3ilkB_
Top template information
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized trna/rrna methyltransferase hi0380;
PDBTitle: the structure of a probable methylase family protein from haemophilus2 influenzae rd kw20
Confidence and coverage
Confidence:100.0% Coverage: 97%
222 residues ( 97% 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  MRITIILVAPARAENIGAAARAMKTMGFSDLRIVDSQAHLEPATRWVAHGSGDIIDNIKV
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Disorder  ?


























































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   .........70.........80.........90.........100.........110.........120
Sequence  FPTLAESLHDVDFTVATTARSRAKYHYYATPVELVPLLEEKSSWMSHAALVFGREDSGLT
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   .........130.........140.........150.........160.........170.........180
Sequence  NEELALADVLTGVPMVADYPSLNLGQAVMVYCYQLATLIQQPAKSDATADQHQLQALRER
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Disorder 

















?

















?
???????????









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   .........190.........200.........210.........220........
Sequence  AMTLLTTLAVADDIKLVDWLQQRLGLLEQRDTAMLHRLLHDIEKNITK
Secondary structure 








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???
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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 3ilk chain B

3D model

Region: 2 - 227
Aligned: 222
Modelled: 216
Confidence: 100.0%
Identity: 28%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized trna/rrna methyltransferase hi0380;
PDBTitle: the structure of a probable methylase family protein from haemophilus2 influenzae rd kw20

Phyre2

PDB 3ic6 chain A

3D model

Region: 2 - 183
Aligned: 180
Modelled: 179
Confidence: 100.0%
Identity: 35%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative methylase family protein;
PDBTitle: crystal structure of putative methylase family protein from neisseria2 gonorrhoeae

Phyre2

PDB 3onp chain A

3D model

Region: 1 - 158
Aligned: 158
Modelled: 153
Confidence: 100.0%
Identity: 37%
PDB header:transferase
Chain: A: PDB Molecule:trna/rrna methyltransferase (spou);
PDBTitle: crystal structure of trna/rrna methyltransferase spou from rhodobacter2 sphaeroides

Phyre2

PDB 1zjr chain A

3D model

Region: 2 - 185
Aligned: 174
Modelled: 183
Confidence: 100.0%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase;
PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme

Phyre2

PDB 1v2x chain A

3D model

Region: 2 - 180
Aligned: 168
Modelled: 168
Confidence: 100.0%
Identity: 23%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2

PDB 3kty chain A

3D model

Region: 1 - 159
Aligned: 155
Modelled: 153
Confidence: 100.0%
Identity: 29%
PDB header:transferase
Chain: A: PDB Molecule:probable methyltransferase;
PDBTitle: crystal structure of probable methyltransferase from bordetella2 pertussis tohama i

Phyre2

PDB 2ha8 chain A

3D model

Region: 2 - 158
Aligned: 148
Modelled: 148
Confidence: 100.0%
Identity: 16%
PDB header:rna binding protein
Chain: A: PDB Molecule:tar (hiv-1) rna loop binding protein;
PDBTitle: methyltransferase domain of human tar (hiv-1) rna binding2 protein 1

Phyre2

PDB 1gz0 chain A domain 1

3D model

Region: 2 - 158
Aligned: 146
Modelled: 157
Confidence: 100.0%
Identity: 18%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2

PDB 1gz0 chain G

3D model

Region: 2 - 158
Aligned: 146
Modelled: 139
Confidence: 100.0%
Identity: 18%
PDB header:transferase
Chain: G: PDB Molecule:hypothetical trna/rrna methyltransferase yjfh;
PDBTitle: 23s ribosomal rna g2251 2'o-methyltransferase rlmb

Phyre2

PDB 2i6d chain A

3D model

Region: 2 - 158
Aligned: 148
Modelled: 147
Confidence: 100.0%
Identity: 19%
PDB header:transferase
Chain: A: PDB Molecule:rna methyltransferase, trmh family;
PDBTitle: the structure of a putative rna methyltransferase of the trmh family2 from porphyromonas gingivalis.

Phyre2

PDB 1ipa chain A

3D model

Region: 1 - 158
Aligned: 146
Modelled: 146
Confidence: 100.0%
Identity: 16%
PDB header:transferase
Chain: A: PDB Molecule:rna 2'-o-ribose methyltransferase;
PDBTitle: crystal structure of rna 2'-o ribose methyltransferase

Phyre2

PDB 1x7p chain B

3D model

Region: 3 - 158
Aligned: 148
Modelled: 148
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: B: PDB Molecule:rrna methyltransferase;
PDBTitle: crystal structure of the spou methyltransferase avirb from2 streptomyces viridochromogenes in complex with the cofactor adomet

Phyre2

PDB 1mxi chain A

3D model

Region: 3 - 164
Aligned: 150
Modelled: 150
Confidence: 100.0%
Identity: 19%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2

PDB 1ipa chain A domain 1

3D model

Region: 3 - 158
Aligned: 144
Modelled: 144
Confidence: 100.0%
Identity: 17%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: SpoU-like RNA 2'-O ribose methyltransferase

Phyre2

PDB 3gyq chain B

3D model

Region: 3 - 158
Aligned: 147
Modelled: 147
Confidence: 100.0%
Identity: 19%
PDB header:transferase
Chain: B: PDB Molecule:rrna (adenosine-2'-o-)-methyltransferase;
PDBTitle: structure of the thiostrepton-resistance methyltransferase2 s-adenosyl-l-methionine complex

Phyre2

PDB 3dcm chain X

3D model

Region: 2 - 155
Aligned: 154
Modelled: 154
Confidence: 100.0%
Identity: 14%
PDB header:transferase
Chain: X: PDB Molecule:uncharacterized protein tm_1570;
PDBTitle: crystal structure of the thermotoga maritima spout family2 rna-methyltransferase protein tm1570 in complex with s-3 adenosyl-l-methionine

Phyre2

PDB 3e5y chain B

3D model

Region: 3 - 164
Aligned: 137
Modelled: 137
Confidence: 100.0%
Identity: 18%
PDB header:transferase
Chain: B: PDB Molecule:trmh family rna methyltransferase;
PDBTitle: crystal structure of trmh family rna methyltransferase from2 burkholderia pseudomallei

Phyre2

PDB 3l8u chain A

3D model

Region: 2 - 167
Aligned: 148
Modelled: 148
Confidence: 100.0%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:putative rrna methylase;
PDBTitle: crystal structure of smu.1707c, a putative rrna methyltransferase from2 streptococcus mutans ua159

Phyre2

PDB 1vhk chain A

3D model

Region: 2 - 155
Aligned: 142
Modelled: 154
Confidence: 97.0%
Identity: 15%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yqeu;
PDBTitle: crystal structure of an hypothetical protein

Phyre2

PDB 1vhk chain A domain 2

3D model

Region: 1 - 161
Aligned: 149
Modelled: 161
Confidence: 96.8%
Identity: 13%
Fold: alpha/beta knot
Superfamily: alpha/beta knot
Family: YggJ C-terminal domain-like

Phyre2
1

c3ilkB_
2

c3ic6A_
3

c3onpA_
4

c1zjrA_
5

d1v2xa_
6

c3ktyA_
7

c2ha8A_
8

d1gz0a1
9

c1gz0G_
10

c2i6dA_
11

c1ipaA_
12

c1x7pB_
13

d1mxia_
14

d1ipaa1
15

c3gyqB_
16

c3dcmX_
17

c3e5yB_
18

c3l8uA_
19

c1vhkA_
20

d1vhka2
21



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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3ilkB_



100.0 28 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized trna/rrna methyltransferase hi0380;
PDBTitle: the structure of a probable methylase family protein from haemophilus2 influenzae rd kw20
2c3ic6A_



100.0 35 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative methylase family protein;
PDBTitle: crystal structure of putative methylase family protein from neisseria2 gonorrhoeae
3c3onpA_



100.0 37 PDB header:transferase
Chain: A: PDB Molecule:trna/rrna methyltransferase (spou);
PDBTitle: crystal structure of trna/rrna methyltransferase spou from rhodobacter2 sphaeroides
4c1zjrA_



100.0 17 PDB header:transferase
Chain: A: PDB Molecule:trna (guanosine-2'-o-)-methyltransferase;
PDBTitle: crystal structure of a. aeolicus trmh/spou trna modifying enzyme
5d1v2xa_



100.0 23 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:SpoU-like RNA 2'-O ribose methyltransferase
6c3ktyA_



100.0 29 PDB header:transferase
Chain: A: PDB Molecule:probable methyltransferase;
PDBTitle: crystal structure of probable methyltransferase from bordetella2 pertussis tohama i
7c2ha8A_



100.0 16 PDB header:rna binding protein
Chain: A: PDB Molecule:tar (hiv-1) rna loop binding protein;
PDBTitle: methyltransferase domain of human tar (hiv-1) rna binding2 protein 1
8d1gz0a1



100.0 18 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:SpoU-like RNA 2'-O ribose methyltransferase
9c1gz0G_



100.0 18 PDB header:transferase
Chain: G: PDB Molecule:hypothetical trna/rrna methyltransferase yjfh;
PDBTitle: 23s ribosomal rna g2251 2'o-methyltransferase rlmb
10c2i6dA_



100.0 19 PDB header:transferase
Chain: A: PDB Molecule:rna methyltransferase, trmh family;
PDBTitle: the structure of a putative rna methyltransferase of the trmh family2 from porphyromonas gingivalis.
11c1ipaA_



100.0 16 PDB header:transferase
Chain: A: PDB Molecule:rna 2'-o-ribose methyltransferase;
PDBTitle: crystal structure of rna 2'-o ribose methyltransferase
12c1x7pB_



100.0 21 PDB header:transferase
Chain: B: PDB Molecule:rrna methyltransferase;
PDBTitle: crystal structure of the spou methyltransferase avirb from2 streptomyces viridochromogenes in complex with the cofactor adomet
13d1mxia_



100.0 19 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:SpoU-like RNA 2'-O ribose methyltransferase
14d1ipaa1



100.0 17 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:SpoU-like RNA 2'-O ribose methyltransferase
15c3gyqB_



100.0 19 PDB header:transferase
Chain: B: PDB Molecule:rrna (adenosine-2'-o-)-methyltransferase;
PDBTitle: structure of the thiostrepton-resistance methyltransferase2 s-adenosyl-l-methionine complex
16c3dcmX_



100.0 14 PDB header:transferase
Chain: X: PDB Molecule:uncharacterized protein tm_1570;
PDBTitle: crystal structure of the thermotoga maritima spout family2 rna-methyltransferase protein tm1570 in complex with s-3 adenosyl-l-methionine
17c3e5yB_



100.0 18 PDB header:transferase
Chain: B: PDB Molecule:trmh family rna methyltransferase;
PDBTitle: crystal structure of trmh family rna methyltransferase from2 burkholderia pseudomallei
18c3l8uA_



100.0 20 PDB header:transferase
Chain: A: PDB Molecule:putative rrna methylase;
PDBTitle: crystal structure of smu.1707c, a putative rrna methyltransferase from2 streptococcus mutans ua159
19c1vhkA_



97.0 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yqeu;
PDBTitle: crystal structure of an hypothetical protein
20d1vhka2



96.8 13 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YggJ C-terminal domain-like
21d1nxza2



not modelled 96.4 15 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YggJ C-terminal domain-like
22c2egwB_



not modelled 95.7 13 PDB header:rna methyltransferase
Chain: B: PDB Molecule:upf0088 protein aq_165;
PDBTitle: crystal structure of rrna methyltransferase with sah ligand
23c3kw2A_



not modelled 95.7 17 PDB header:transferase
Chain: A: PDB Molecule:probable r-rna methyltransferase;
PDBTitle: crystal structure of probable rrna-methyltransferase from2 porphyromonas gingivalis
24c1vhyB_



not modelled 95.5 14 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein hi0303;
PDBTitle: crystal structure of haemophilus influenzae protein hi0303, pfam2 duf558
25d1v6za2



not modelled 95.2 17 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YggJ C-terminal domain-like
26c2yy8B_



not modelled 94.7 17 PDB header:transferase
Chain: B: PDB Molecule:upf0106 protein ph0461;
PDBTitle: crystal structure of archaeal trna-methylase for position2 56 (atrm56) from pyrococcus horikoshii, complexed with s-3 adenosyl-l-methionine
27c2cx8B_



not modelled 94.6 18 PDB header:transferase
Chain: B: PDB Molecule:methyl transferase;
PDBTitle: crystal structure of methyltransferase with ligand(sah)
28d2o3aa1



not modelled 93.6 17 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:AF0751-like
29d1duvg2



not modelled 85.0 20 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
30d1otha2



not modelled 84.4 14 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
31d1pvva2



not modelled 84.1 11 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
32c3d6nB_



not modelled 82.6 9 PDB header:hydrolase/transferase
Chain: B: PDB Molecule:aspartate carbamoyltransferase;
PDBTitle: crystal structure of aquifex dihydroorotase activated by aspartate2 transcarbamoylase
33d1js1x2



not modelled 81.9 16 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
34c1a1sA_



not modelled 81.2 11 PDB header:transcarbamylase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: ornithine carbamoyltransferase from pyrococcus furiosus
35d1dxha2



not modelled 80.3 13 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
36d1ml4a2



not modelled 80.2 14 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
37d1pg5a2



not modelled 78.2 12 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
38c2otcA_



not modelled 77.5 21 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: ornithine transcarbamoylase complexed with n-2 (phosphonacetyl)-l-ornithine
39c2w37A_



not modelled 76.2 12 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase, catabolic;
PDBTitle: crystal structure of the hexameric catabolic ornithine2 transcarbamylase from lactobacillus hilgardii
40c1z85B_



not modelled 74.4 13 PDB header:transferase
Chain: B: PDB Molecule:hypothetical protein tm1380;
PDBTitle: crystal structure of a predicted rna methyltransferase (tm1380) from2 thermotoga maritima msb8 at 2.12 a resolution
41d1ekxa2



not modelled 74.0 15 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
42d1vlva2



not modelled 72.3 9 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
43c1pg5A_



not modelled 72.1 12 PDB header:transferase
Chain: A: PDB Molecule:aspartate carbamoyltransferase;
PDBTitle: crystal structure of the unligated (t-state) aspartate2 transcarbamoylase from the extremely thermophilic archaeon sulfolobus3 acidocaldarius
44c2p2gD_



not modelled 69.8 18 PDB header:transferase
Chain: D: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: crystal structure of ornithine carbamoyltransferase from mycobacterium2 tuberculosis (rv1656): orthorhombic form
45c1vlvA_



not modelled 66.8 11 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: crystal structure of ornithine carbamoyltransferase (tm1097) from2 thermotoga maritima at 2.25 a resolution
46c1k3rA_



not modelled 64.0 27 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved protein mt0001;
PDBTitle: crystal structure of the methyltransferase with a knot from2 methanobacterium thermoautotrophicum
47c3updA_



not modelled 63.7 20 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: 2.9 angstrom crystal structure of ornithine carbamoyltransferase2 (argf) from vibrio vulnificus
48c1a5zA_



not modelled 62.8 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-lactate dehydrogenase;
PDBTitle: lactate dehydrogenase from thermotoga maritima (tmldh)
49d1up7a1



not modelled 62.2 10 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
50c2omeA_



not modelled 61.0 25 PDB header:oxidoreductase
Chain: A: PDB Molecule:c-terminal-binding protein 2;
PDBTitle: crystal structure of human ctbp2 dehydrogenase complexed with nad(h)
51c1fvoB_



not modelled 60.4 14 PDB header:transferase
Chain: B: PDB Molecule:ornithine transcarbamylase;
PDBTitle: crystal structure of human ornithine transcarbamylase complexed with2 carbamoyl phosphate
52c1ortD_



not modelled 60.3 16 PDB header:transferase
Chain: D: PDB Molecule:ornithine transcarbamoylase;
PDBTitle: ornithine transcarbamoylase from pseudomonas aeruginosa
53d1ygya1



not modelled 59.3 26 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
54c1ml4A_



not modelled 59.0 14 PDB header:transferase
Chain: A: PDB Molecule:aspartate transcarbamoylase;
PDBTitle: the pala-liganded aspartate transcarbamoylase catalytic subunit from2 pyrococcus abyssi
55c2rgwD_



not modelled 59.0 15 PDB header:transferase
Chain: D: PDB Molecule:aspartate carbamoyltransferase;
PDBTitle: catalytic subunit of m. jannaschii aspartate2 transcarbamoylase
56c3n7uD_



not modelled 58.9 23 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
57c2v6bB_



not modelled 58.8 19 PDB header:oxidoreductase
Chain: B: PDB Molecule:l-lactate dehydrogenase;
PDBTitle: crystal structure of lactate dehydrogenase from deinococcus2 radiodurans (apo form)
58c2g76A_



not modelled 58.5 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of human 3-phosphoglycerate dehydrogenase
59d1k3ra2



not modelled 56.8 27 Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:Hypothetical protein MTH1 (MT0001), dimerisation domain
60c3gg9C_



not modelled 56.6 16 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
61c2nacA_



not modelled 56.0 19 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
62d1obba1



not modelled 55.4 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
63c3grfA_



not modelled 55.3 15 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: x-ray structure of ornithine transcarbamoylase from giardia2 lamblia
64c3evtA_



not modelled 53.8 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from2 lactobacillus plantarum
65d2naca1



not modelled 53.3 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
66c3bazA_



not modelled 53.3 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:hydroxyphenylpyruvate reductase;
PDBTitle: structure of hydroxyphenylpyruvate reductase from coleus blumei in2 complex with nadp+
67d1qp8a1



not modelled 53.1 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
68d1sc6a1



not modelled 51.0 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
69d1mx3a1



not modelled 51.0 24 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
70c1js1Z_



not modelled 49.6 13 PDB header:transferase
Chain: Z: PDB Molecule:transcarbamylase;
PDBTitle: crystal structure of a new transcarbamylase from the2 anaerobic bacterium bacteroides fragilis at 2.0 a3 resolution
71c1d4fD_



not modelled 48.6 17 PDB header:hydrolase
Chain: D: PDB Molecule:s-adenosylhomocysteine hydrolase;
PDBTitle: crystal structure of recombinant rat-liver d244e mutant s-2 adenosylhomocysteine hydrolase
72c1j4aA_



not modelled 47.7 16 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
73c1zq2A_



not modelled 45.3 17 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: crystal structure of n-acetyl-l-ornithine transcarbamylase2 complexed with cp
74c3ijpA_



not modelled 45.1 9 PDB header:oxidoreductase
Chain: A: PDB Molecule:dihydrodipicolinate reductase;
PDBTitle: crystal structure of dihydrodipicolinate reductase from2 bartonella henselae at 2.0a resolution
75d1gdha1



not modelled 44.2 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
76c3gvpB_



not modelled 42.1 19 PDB header:hydrolase
Chain: B: PDB Molecule:adenosylhomocysteinase 3;
PDBTitle: human sahh-like domain of human adenosylhomocysteinase 3
77c1qp8A_



not modelled 40.3 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase;
PDBTitle: crystal structure of a putative formate dehydrogenase from2 pyrobaculum aerophilum
78c2pwzG_



not modelled 40.1 18 PDB header:oxidoreductase
Chain: G: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of the apo form of e.coli malate dehydrogenase
79c3gd5D_



not modelled 40.0 8 PDB header:transferase
Chain: D: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: crystal structure of ornithine carbamoyltransferase from gloeobacter2 violaceus
80c1gdhA_



not modelled 39.8 15 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
81d2at2a2



not modelled 39.7 8 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
82c1wwkA_



not modelled 39.4 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of phosphoglycerate dehydrogenase from pyrococcus2 horikoshii ot3
83d1a5za1



not modelled 39.4 11 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
84d1u8xx1



not modelled 38.9 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
85d2cmda1



not modelled 38.6 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
86d1gpja2



not modelled 38.4 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Aminoacid dehydrogenase-like, C-terminal domain
87d1j4aa1



not modelled 37.5 16 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
88c3q98A_



not modelled 35.7 10 PDB header:transferase
Chain: A: PDB Molecule:transcarbamylase;
PDBTitle: structure of ygew encoded protein from e. coli
89c2gcgB_



not modelled 35.2 24 PDB header:oxidoreductase
Chain: B: PDB Molecule:glyoxylate reductase/hydroxypyruvate reductase;
PDBTitle: ternary crystal structure of human glyoxylate2 reductase/hydroxypyruvate reductase
90c3hg7A_



not modelled 34.4 24 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
91d7reqb2



not modelled 31.4 15 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
92c2j6iC_



not modelled 31.4 23 PDB header:oxidoreductase
Chain: C: PDB Molecule:formate dehydrogenase;
PDBTitle: candida boidinii formate dehydrogenase (fdh) c-terminal2 mutant
93d1tuga1



not modelled 30.9 10 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
94c2pi1C_



not modelled 30.9 20 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
95d1s6ya1



not modelled 30.3 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
96c1mldA_



not modelled 29.8 20 PDB header:oxidoreductase(nad(a)-choh(d))
Chain: A: PDB Molecule:malate dehydrogenase;
PDBTitle: refined structure of mitochondrial malate dehydrogenase2 from porcine heart and the consensus structure for3 dicarboxylic acid oxidoreductases
97c2d0iC_



not modelled 29.0 22 PDB header:oxidoreductase
Chain: C: PDB Molecule:dehydrogenase;
PDBTitle: crystal structure ph0520 protein from pyrococcus horikoshii ot3
98d1diha1



not modelled 28.8 13 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
99c2dbqA_



not modelled 28.8 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:glyoxylate reductase;
PDBTitle: crystal structure of glyoxylate reductase (ph0597) from pyrococcus2 horikoshii ot3, complexed with nadp (i41)
100c2y0fD_



not modelled 28.0 24 PDB header:oxidoreductase
Chain: D: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase;
PDBTitle: structure of gcpe (ispg) from thermus thermophilus hb27
101c3lxmC_



not modelled 27.9 19 PDB header:transferase
Chain: C: PDB Molecule:aspartate carbamoyltransferase;
PDBTitle: 2.00 angstrom resolution crystal structure of a catalytic2 subunit of an aspartate carbamoyltransferase (pyrb) from3 yersinia pestis co92
102c3sdsA_



not modelled 27.9 18 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase, mitochondrial;
PDBTitle: crystal structure of a mitochondrial ornithine carbamoyltransferase2 from coccidioides immitis
103c3dhyC_



not modelled 27.9 22 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
104c1ybaC_



not modelled 27.3 23 PDB header:oxidoreductase
Chain: C: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: the active form of phosphoglycerate dehydrogenase
105c2w2kB_



not modelled 26.2 17 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.
106c2cukC_



not modelled 25.7 24 PDB header:oxidoreductase
Chain: C: PDB Molecule:glycerate dehydrogenase/glyoxylate reductase;
PDBTitle: crystal structure of tt0316 protein from thermus thermophilus hb8
107d2dlda1



not modelled 25.5 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Formate/glycerate dehydrogenases, NAD-domain
108c1dxyA_



not modelled 25.2 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-2-hydroxyisocaproate dehydrogenase;
PDBTitle: structure of d-2-hydroxyisocaproate dehydrogenase
109c2eklA_



not modelled 24.5 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: structure of st1218 protein from sulfolobus tokodaii
110c8ldhA_



not modelled 24.5 18 PDB header:oxidoreductase(choh(d)-nad(a))
Chain: A: PDB Molecule:m4 apo-lactate dehydrogenase;
PDBTitle: refined crystal structure of dogfish m4 apo-lactate2 dehydrogenase
111c3ckyA_



not modelled 23.6 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-hydroxymethyl glutarate dehydrogenase;
PDBTitle: structural and kinetic properties of a beta-hydroxyacid dehydrogenase2 involved in nicotinate fermentation
112c1xdwA_



not modelled 23.2 23 PDB header:oxidoreductase
Chain: A: PDB Molecule:nad+-dependent (r)-2-hydroxyglutarate
PDBTitle: nad+-dependent (r)-2-hydroxyglutarate dehydrogenase from2 acidaminococcus fermentans
113d1o94c_



not modelled 21.8 18 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Adenine nucleotide alpha hydrolases-like
Family:ETFP subunits
114c3oirA_



not modelled 21.4 15 PDB header:transport protein
Chain: A: PDB Molecule:sulfate transporter sulfate transporter family protein;
PDBTitle: crystal structure of sulfate transporter family protein from wolinella2 succinogenes
115c2v3jA_



not modelled 21.4 18 PDB header:ribosomal protein
Chain: A: PDB Molecule:essential for mitotic growth 1;
PDBTitle: the yeast ribosome synthesis factor emg1 alpha beta knot2 fold methyltransferase
116c3kboB_



not modelled 20.9 22 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
117c3n58D_



not modelled 20.8 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

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite



Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0