Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP21893
DateThu Jan 5 11:38:41 GMT 2012
Unique Job IDf6be5d885ee26dad

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2zxrA_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj;
PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8
Confidence and coverage
Confidence:100.0% Coverage: 83%
481 residues ( 83% 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  MKQQIQLRRREVDETADLPAELPPLLRRLYASRGVRSAQELERSVKGMLPWQQLSGVEKA
Secondary structure 
























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Disorder  ???????

?
???













































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   .........70.........80.........90.........100.........110.........120
Sequence  VEILYNAFREGTRIIVVGDFDADGATSTALSVLAMRSLGCSNIDYLVPNRFEDGYGLSPE
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??


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   .........130.........140.........150.........160.........170.........180
Sequence  VVDQAHARGAQLIVTVDNGISSHAGVEHARSLGIPVIVTDHHLPGDTLPAAEAIINPNLR
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   .........190.........200.........210.........220.........230.........240
Sequence  DCNFPSKSLAGVGVAFYLMLALRTFLRDQGWFDERNIAIPNLAELLDLVALGTVADVVPL
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?

??
?????




















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   .........250.........260.........270.........280.........290.........300
Sequence  DANNRILTWQGMSRIRAGKCRPGIKALLEVANRDAQKLAASDLGFALGPRLNAAGRLDDM
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   .........310.........320.........330.........340.........350.........360
Sequence  SVGVALLLCDNIGEARVLANELDALNQTRKEIEQGMQIEALTLCEKLERSRDTLPGGLAM
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   .........370.........380.........390.........400.........410.........420
Sequence  YHPEWHQGVVGILASRIKERFHRPVIAFAPAGDGTLKGSGRSIQGLHMRDALERLDTLYP
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   .........430.........440.........450.........460.........470.........480
Sequence  GMMLKFGGHAMAAGLSLEEDKFKLFQQRFGELVTEWLDPSLLQGEVVSDGPLSPAEMTME
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   .........490.........500.........510.........520.........530.........540
Sequence  VAQLLRDAGPWGQMFPEPLFDGHFRLLQQRLVGERHLKVMVEPVGGGPLLDGIAFNVDTA
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   .........550.........560.........570.......
Sequence  LWPDNGVREVQLAYKLDINEFRGNRSLQIIIDNIWPI
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 2zxr chain A

3D model

Region: 2 - 576
Aligned: 481
Modelled: 517
Confidence: 100.0%
Identity: 35%
PDB header:hydrolase
Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj;
PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8

Phyre2

PDB 1ir6 chain A

3D model

Region: 49 - 468
Aligned: 384
Modelled: 413
Confidence: 100.0%
Identity: 38%
Fold: DHH phosphoesterases
Superfamily: DHH phosphoesterases
Family: Exonuclease RecJ

Phyre2

PDB 1ir6 chain A

3D model

Region: 49 - 468
Aligned: 384
Modelled: 413
Confidence: 100.0%
Identity: 38%
PDB header:hydrolase
Chain: A: PDB Molecule:exonuclease recj;
PDBTitle: crystal structure of exonuclease recj bound to manganese

Phyre2

PDB 3dma chain A

3D model

Region: 58 - 455
Aligned: 309
Modelled: 319
Confidence: 100.0%
Identity: 16%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:exopolyphosphatase-related protein;
PDBTitle: crystal structure of an exopolyphosphatase-related protein2 from bacteroides fragilis. northeast structural genomics3 target bfr192

Phyre2

PDB 3dev chain B

3D model

Region: 59 - 455
Aligned: 301
Modelled: 317
Confidence: 100.0%
Identity: 16%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:sh1221;
PDBTitle: crystal structure of sh1221 protein from staphylococcus haemolyticus,2 northeast structural genomics consortium target shr87

Phyre2

PDB 1wpn chain A

3D model

Region: 72 - 244
Aligned: 146
Modelled: 158
Confidence: 98.0%
Identity: 13%
Fold: DHH phosphoesterases
Superfamily: DHH phosphoesterases
Family: Manganese-dependent inorganic pyrophosphatase (family II)

Phyre2

PDB 1i74 chain A

3D model

Region: 73 - 244
Aligned: 139
Modelled: 150
Confidence: 98.0%
Identity: 19%
Fold: DHH phosphoesterases
Superfamily: DHH phosphoesterases
Family: Manganese-dependent inorganic pyrophosphatase (family II)

Phyre2

PDB 1k20 chain A

3D model

Region: 73 - 244
Aligned: 139
Modelled: 154
Confidence: 97.7%
Identity: 15%
Fold: DHH phosphoesterases
Superfamily: DHH phosphoesterases
Family: Manganese-dependent inorganic pyrophosphatase (family II)

Phyre2

PDB 2haw chain A domain 1

3D model

Region: 72 - 244
Aligned: 141
Modelled: 156
Confidence: 97.6%
Identity: 11%
Fold: DHH phosphoesterases
Superfamily: DHH phosphoesterases
Family: Manganese-dependent inorganic pyrophosphatase (family II)

Phyre2

PDB 2eb0 chain B

3D model

Region: 74 - 244
Aligned: 141
Modelled: 143
Confidence: 97.3%
Identity: 16%
PDB header:hydrolase
Chain: B: PDB Molecule:manganese-dependent inorganic pyrophosphatase;
PDBTitle: crystal structure of methanococcus jannaschii putative family ii2 inorganic pyrophosphatase

Phyre2

PDB 2zvf chain G

3D model

Region: 312 - 456
Aligned: 139
Modelled: 145
Confidence: 95.8%
Identity: 14%
PDB header:ligase
Chain: G: PDB Molecule:alanyl-trna synthetase;
PDBTitle: crystal structure of archaeoglobus fulgidus alanyl-trna2 synthetase c-terminal dimerization domain

Phyre2

PDB 2qb6 chain A

3D model

Region: 64 - 236
Aligned: 148
Modelled: 160
Confidence: 94.3%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:exopolyphosphatase;
PDBTitle: saccharomyces cerevisiae cytosolic exopolyphosphatase, sulfate complex

Phyre2

PDB 2fyw chain A domain 1

3D model

Region: 74 - 162
Aligned: 84
Modelled: 89
Confidence: 91.9%
Identity: 19%
Fold: NIF3 (NGG1p interacting factor 3)-like
Superfamily: NIF3 (NGG1p interacting factor 3)-like
Family: NIF3 (NGG1p interacting factor 3)-like

Phyre2

PDB 1x94 chain A

3D model

Region: 38 - 206
Aligned: 162
Modelled: 169
Confidence: 91.7%
Identity: 14%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2

PDB 1nri chain A

3D model

Region: 54 - 257
Aligned: 183
Modelled: 175
Confidence: 91.3%
Identity: 20%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein hi0754;
PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae

Phyre2

PDB 1nri chain A

3D model

Region: 54 - 257
Aligned: 183
Modelled: 175
Confidence: 91.3%
Identity: 20%
Fold: SIS domain
Superfamily: SIS domain
Family: mono-SIS domain

Phyre2

PDB 2yva chain B

3D model

Region: 55 - 159
Aligned: 102
Modelled: 105
Confidence: 89.8%
Identity: 14%
PDB header:dna binding protein
Chain: B: PDB Molecule:dnaa initiator-associating protein diaa;
PDBTitle: crystal structure of escherichia coli diaa

Phyre2

PDB 1nmp chain A

3D model

Region: 85 - 162
Aligned: 73
Modelled: 76
Confidence: 89.6%
Identity: 21%
Fold: NIF3 (NGG1p interacting factor 3)-like
Superfamily: NIF3 (NGG1p interacting factor 3)-like
Family: NIF3 (NGG1p interacting factor 3)-like

Phyre2

PDB 1qo2 chain A

3D model

Region: 91 - 160
Aligned: 68
Modelled: 70
Confidence: 88.2%
Identity: 18%
Fold: TIM beta/alpha-barrel
Superfamily: Ribulose-phoshate binding barrel
Family: Histidine biosynthesis enzymes

Phyre2

PDB 2gx8 chain A domain 1

3D model

Region: 58 - 162
Aligned: 99
Modelled: 105
Confidence: 85.4%
Identity: 19%
Fold: NIF3 (NGG1p interacting factor 3)-like
Superfamily: NIF3 (NGG1p interacting factor 3)-like
Family: NIF3 (NGG1p interacting factor 3)-like

Phyre2
1

c2zxrA_
2

d1ir6a_
3

c1ir6A_
4

c3dmaA_
5

c3devB_
6

d1wpna_
7

d1i74a_
8

d1k20a_
9

d2hawa1
10

c2eb0B_
11

c2zvfG_
12

c2qb6A_
13

d2fywa1
14

d1x94a_
15

c1nriA_
16

d1nria_
17

c2yvaB_
18

d1nmpa_
19

d1qo2a_
20

d2gx8a1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2zxrA_



100.0 35 PDB header:hydrolase
Chain: A: PDB Molecule:single-stranded dna specific exonuclease recj;
PDBTitle: crystal structure of recj in complex with mg2+ from thermus2 thermophilus hb8
2d1ir6a_



100.0 38 Fold:DHH phosphoesterases
Superfamily:DHH phosphoesterases
Family:Exonuclease RecJ
3c1ir6A_



100.0 38 PDB header:hydrolase
Chain: A: PDB Molecule:exonuclease recj;
PDBTitle: crystal structure of exonuclease recj bound to manganese
4c3dmaA_



100.0 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:exopolyphosphatase-related protein;
PDBTitle: crystal structure of an exopolyphosphatase-related protein2 from bacteroides fragilis. northeast structural genomics3 target bfr192
5c3devB_



100.0 16 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:sh1221;
PDBTitle: crystal structure of sh1221 protein from staphylococcus haemolyticus,2 northeast structural genomics consortium target shr87
6d1wpna_



98.0 13 Fold:DHH phosphoesterases
Superfamily:DHH phosphoesterases
Family:Manganese-dependent inorganic pyrophosphatase (family II)
7d1i74a_



98.0 19 Fold:DHH phosphoesterases
Superfamily:DHH phosphoesterases
Family:Manganese-dependent inorganic pyrophosphatase (family II)
8d1k20a_



97.7 15 Fold:DHH phosphoesterases
Superfamily:DHH phosphoesterases
Family:Manganese-dependent inorganic pyrophosphatase (family II)
9d2hawa1



97.6 11 Fold:DHH phosphoesterases
Superfamily:DHH phosphoesterases
Family:Manganese-dependent inorganic pyrophosphatase (family II)
10c2eb0B_



97.3 16 PDB header:hydrolase
Chain: B: PDB Molecule:manganese-dependent inorganic pyrophosphatase;
PDBTitle: crystal structure of methanococcus jannaschii putative family ii2 inorganic pyrophosphatase
11c2zvfG_



95.8 14 PDB header:ligase
Chain: G: PDB Molecule:alanyl-trna synthetase;
PDBTitle: crystal structure of archaeoglobus fulgidus alanyl-trna2 synthetase c-terminal dimerization domain
12c2qb6A_



94.3 18 PDB header:hydrolase
Chain: A: PDB Molecule:exopolyphosphatase;
PDBTitle: saccharomyces cerevisiae cytosolic exopolyphosphatase, sulfate complex
13d2fywa1



91.9 19 Fold:NIF3 (NGG1p interacting factor 3)-like
Superfamily:NIF3 (NGG1p interacting factor 3)-like
Family:NIF3 (NGG1p interacting factor 3)-like
14d1x94a_



91.7 14 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
15c1nriA_



91.3 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein hi0754;
PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae
16d1nria_



91.3 20 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
17c2yvaB_



89.8 14 PDB header:dna binding protein
Chain: B: PDB Molecule:dnaa initiator-associating protein diaa;
PDBTitle: crystal structure of escherichia coli diaa
18d1nmpa_



89.6 21 Fold:NIF3 (NGG1p interacting factor 3)-like
Superfamily:NIF3 (NGG1p interacting factor 3)-like
Family:NIF3 (NGG1p interacting factor 3)-like
19d1qo2a_



88.2 18 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
20d2gx8a1



85.4 19 Fold:NIF3 (NGG1p interacting factor 3)-like
Superfamily:NIF3 (NGG1p interacting factor 3)-like
Family:NIF3 (NGG1p interacting factor 3)-like
21d1h5ya_



not modelled 85.2 19 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
22c3g98B_



not modelled 85.2 14 PDB header:ligase
Chain: B: PDB Molecule:alanyl-trna synthetase;
PDBTitle: crystal structure of the c-ala domain from aquifex aeolicus2 alanyl-trna synthetase
23c2nydB_



not modelled 84.4 20 PDB header:unknown function
Chain: B: PDB Molecule:upf0135 protein sa1388;
PDBTitle: crystal structure of staphylococcus aureus hypothetical protein sa1388
24c2ihfA_



not modelled 84.0 11 PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of deletion mutant delta 228-252 r190a of the2 single-stranded dna binding protein from thermus aquaticus
25d2jfga1



not modelled 83.4 18 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
26c3trjC_



not modelled 83.3 16 PDB header:isomerase
Chain: C: PDB Molecule:phosphoheptose isomerase;
PDBTitle: structure of a phosphoheptose isomerase from francisella tularensis
27d1tk9a_



not modelled 82.1 16 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
28c1ecjB_



not modelled 81.8 19 PDB header:transferase
Chain: B: PDB Molecule:glutamine phosphoribosylpyrophosphate
PDBTitle: escherichia coli glutamine phosphoribosylpyrophosphate2 (prpp) amidotransferase complexed with 2 amp per tetramer
29c2gx8B_



not modelled 81.2 19 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:nif3-related protein;
PDBTitle: the crystal stucture of bacillus cereus protein related to nif3
30c2w6rA_



not modelled 80.8 13 PDB header:lyase
Chain: A: PDB Molecule:imidazole glycerol phosphate synthase subunit
PDBTitle: crystal structure of an artificial (ba)8-barrel protein2 designed from identical half barrels
31c3cvjB_



not modelled 79.0 18 PDB header:isomerase
Chain: B: PDB Molecule:putative phosphoheptose isomerase;
PDBTitle: crystal structure of a putative phosphoheptose isomerase (bh3325) from2 bacillus halodurans c-125 at 2.00 a resolution
32d1vzwa1



not modelled 78.5 18 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
33c3pdiG_



not modelled 78.4 11 PDB header:protein binding
Chain: G: PDB Molecule:nitrogenase mofe cofactor biosynthesis protein nife;
PDBTitle: precursor bound nifen
34c3kf6A_



not modelled 78.1 20 PDB header:structural protein
Chain: A: PDB Molecule:protein stn1;
PDBTitle: crystal structure of s. pombe stn1-ten1 complex
35c2iheA_



not modelled 78.0 9 PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of wild-type single-stranded dna binding protein2 from thermus aquaticus
36d1y5ia2



not modelled 77.9 14 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
37d1p3da1



not modelled 77.5 21 Fold:MurCD N-terminal domain
Superfamily:MurCD N-terminal domain
Family:MurCD N-terminal domain
38c3q98A_



not modelled 77.4 22 PDB header:transferase
Chain: A: PDB Molecule:transcarbamylase;
PDBTitle: structure of ygew encoded protein from e. coli
39d1m3sa_



not modelled 77.4 15 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
40c3ippA_



not modelled 76.5 19 PDB header:transferase
Chain: A: PDB Molecule:putative thiosulfate sulfurtransferase ynje;
PDBTitle: crystal structure of sulfur-free ynje
41c1zq2A_



not modelled 76.3 18 PDB header:transferase
Chain: A: PDB Molecule:ornithine carbamoyltransferase;
PDBTitle: crystal structure of n-acetyl-l-ornithine transcarbamylase2 complexed with cp
42d1x92a_



not modelled 76.3 13 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
43d1u9ya1



not modelled 75.9 16 Fold:PRTase-like
Superfamily:PRTase-like
Family:Phosphoribosylpyrophosphate synthetase-like
44d1pvda1



not modelled 74.4 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
45c2p4dA_



not modelled 74.0 10 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity protein phosphatase;
PDBTitle: structure-assisted discovery of variola major h12 phosphatase inhibitors
46c3tdmD_



not modelled 73.8 15 PDB header:de novo protein
Chain: D: PDB Molecule:computationally designed two-fold symmetric tim-barrel
PDBTitle: computationally designed tim-barrel protein, halfflr
47d1dkua1



not modelled 73.6 11 Fold:PRTase-like
Superfamily:PRTase-like
Family:Phosphoribosylpyrophosphate synthetase-like
48d1ovma1



not modelled 72.6 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
49c3fhwB_



not modelled 72.4 13 PDB header:dna binding protein
Chain: B: PDB Molecule:primosomal replication protein n;
PDBTitle: crystal structure of the protein prib from bordetella parapertussis.2 northeast structural genomics consortium target bpr162.
50c3guxA_



not modelled 72.1 20 PDB header:hydrolase
Chain: A: PDB Molecule:putative zn-dependent exopeptidase;
PDBTitle: crystal structure of a putative zn-dependent exopeptidase (bvu_1317)2 from bacteroides vulgatus atcc 8482 at 1.80 a resolution
51c3ke8A_



not modelled 72.0 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-enyl diphosphate
PDBTitle: crystal structure of isph:hmbpp-complex
52d1a9xb2



not modelled 71.9 15 Fold:Flavodoxin-like
Superfamily:Class I glutamine amidotransferase-like
Family:Class I glutamine amidotransferases (GAT)
53c1keeH_



not modelled 71.7 15 PDB header:ligase
Chain: H: PDB Molecule:carbamoyl-phosphate synthetase small chain;
PDBTitle: inactivation of the amidotransferase activity of carbamoyl phosphate2 synthetase by the antibiotic acivicin
54d1pqua1



not modelled 70.9 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
55d1iuka_



not modelled 70.8 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
56c2decA_



not modelled 70.8 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:325aa long hypothetical protein;
PDBTitle: crystal structure of the ph0510 protein from pyrococcus horikoshii ot3
57d1thfd_



not modelled 70.2 15 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
58c3k8aA_



not modelled 69.5 13 PDB header:dna binding protein
Chain: A: PDB Molecule:putative primosomal replication protein;
PDBTitle: neisseria gonorrhoeae prib
59c2ivfA_



not modelled 68.4 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum
60c3izbA_



not modelled 68.4 19 PDB header:ribosome
Chain: A: PDB Molecule:40s ribosomal protein rps0 (s2p);
PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
61d1vlva2



not modelled 68.3 26 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
62c3olhA_



not modelled 67.9 20 PDB header:transferase
Chain: A: PDB Molecule:3-mercaptopyruvate sulfurtransferase;
PDBTitle: human 3-mercaptopyruvate sulfurtransferase
63d2ji7a1



not modelled 67.4 10 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
64c2v45A_



not modelled 67.2 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: a new catalytic mechanism of periplasmic nitrate reductase2 from desulfovibrio desulfuricans atcc 27774 from3 crystallographic and epr data and based on detailed4 analysis of the sixth ligand
65c2x3yA_



not modelled 66.6 14 PDB header:isomerase
Chain: A: PDB Molecule:phosphoheptose isomerase;
PDBTitle: crystal structure of gmha from burkholderia pseudomallei
66c3eafA_



not modelled 66.3 11 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein;
PDBTitle: crystal structure of abc transporter, substrate binding protein2 aeropyrum pernix
67c3fxaA_



not modelled 66.0 15 PDB header:sugar binding protein
Chain: A: PDB Molecule:sis domain protein;
PDBTitle: crystal structure of a putative sugar-phosphate isomerase2 (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 a3 resolution
68d2jioa2



not modelled 66.0 10 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
69d1gm5a2



not modelled 65.8 11 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RecG "wedge" domain
70c3gdwA_



not modelled 65.0 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:sigma-54 interaction domain protein;
PDBTitle: crystal structure of sigma-54 interaction domain protein from2 enterococcus faecalis
71c2xhzC_



not modelled 64.6 15 PDB header:isomerase
Chain: C: PDB Molecule:arabinose 5-phosphate isomerase;
PDBTitle: probing the active site of the sugar isomerase domain from e. coli2 arabinose-5-phosphate isomerase via x-ray crystallography
72c3cwoX_



not modelled 64.3 21 PDB header:de novo protein
Chain: X: PDB Molecule:beta/alpha-barrel protein based on 1thf and 1tmy;
PDBTitle: a beta/alpha-barrel built by the combination of fragments2 from different folds
73d1u9ya2



not modelled 64.1 16 Fold:PRTase-like
Superfamily:PRTase-like
Family:Phosphoribosylpyrophosphate synthetase-like
74d1jeoa_



not modelled 64.0 11 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
75c1z9fA_



not modelled 63.6 7 PDB header:dna binding protein
Chain: A: PDB Molecule:single-strand binding protein;
PDBTitle: crystal structure of single stranded dna-binding protein (tm0604) from2 thermotoga maritima at 2.60 a resolution
76d1urha2



not modelled 63.2 16 Fold:Rhodanese/Cell cycle control phosphatase
Superfamily:Rhodanese/Cell cycle control phosphatase
Family:Multidomain sulfurtransferase (rhodanese)
77c3h75A_



not modelled 62.8 14 PDB header:sugar binding protein
Chain: A: PDB Molecule:periplasmic sugar-binding domain protein;
PDBTitle: crystal structure of a periplasmic sugar-binding protein from the2 pseudomonas fluorescens
78c2y85D_



not modelled 62.8 17 PDB header:isomerase
Chain: D: PDB Molecule:phosphoribosyl isomerase a;
PDBTitle: crystal structure of mycobacterium tuberculosis phosphoribosyl2 isomerase with bound rcdrp
79d1ka9f_



not modelled 62.4 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
80d1eyea_



not modelled 62.3 19 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
81c1dkrB_



not modelled 62.1 11 PDB header:transferase
Chain: B: PDB Molecule:phosphoribosyl pyrophosphate synthetase;
PDBTitle: crystal structures of bacillus subtilis phosphoribosylpyrophosphate2 synthetase: molecular basis of allosteric inhibition and activation.
82c3shoA_



not modelled 61.8 17 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, rpir family;
PDBTitle: crystal structure of rpir transcription factor from sphaerobacter2 thermophilus (sugar isomerase domain)
83c3qy6A_



not modelled 61.8 37 PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase ywqe;
PDBTitle: crystal structures of ywqe from bacillus subtilis and cpsb from2 streptococcus pneumoniae, unique metal-dependent tyrosine3 phosphatases
84d1ml4a2



not modelled 61.4 14 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
85d1o6ca_



not modelled 61.4 15 Fold:UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase
Family:UDP-N-acetylglucosamine 2-epimerase
86c1urhA_



not modelled 60.7 15 PDB header:transferase
Chain: A: PDB Molecule:3-mercaptopyruvate sulfurtransferase;
PDBTitle: the "rhodanese" fold and catalytic mechanism of2 3-mercaptopyruvate sulfotransferases: crystal structure3 of ssea from escherichia coli
87c2zkqb_



not modelled 60.1 18 PDB header:ribosomal protein/rna
Chain: B: PDB Molecule:rna expansion segment es3;
PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
88c1s1hB_



not modelled 59.8 18 PDB header:ribosome
Chain: B: PDB Molecule:40s ribosomal protein s0-a;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.
89d1edga_



not modelled 59.7 22 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
90c3lpnB_



not modelled 59.1 19 PDB header:transferase
Chain: B: PDB Molecule:ribose-phosphate pyrophosphokinase;
PDBTitle: crystal structure of the phosphoribosylpyrophosphate (prpp) synthetase2 from thermoplasma volcanium in complex with an atp analog (ampcpp).
91c3iz6A_



not modelled 59.0 17 PDB header:ribosome
Chain: A: PDB Molecule:40s ribosomal protein sa (s2p);
PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
92d1ozha1



not modelled 58.7 9 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
93d2ihta1



not modelled 58.5 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
94c1yz4A_



not modelled 58.3 12 PDB header:hydrolase
Chain: A: PDB Molecule:dual specificity phosphatase-like 15 isoform a;
PDBTitle: crystal structure of dusp15
95c1boiA_



not modelled 57.9 13 PDB header:transferase
Chain: A: PDB Molecule:rhodanese;
PDBTitle: n-terminally truncated rhodanese
96c2yybA_



not modelled 57.9 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein ttha1606;
PDBTitle: crystal structure of ttha1606 from thermus thermophilus hb8
97c3nuhB_



not modelled 57.8 25 PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit b;
PDBTitle: a domain insertion in e. coli gyrb adopts a novel fold that plays a2 critical role in gyrase function
98d2pi2a1



not modelled 57.2 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
99d1ybha1



not modelled 57.2 9 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
100c3outC_



not modelled 57.0 12 PDB header:isomerase
Chain: C: PDB Molecule:glutamate racemase;
PDBTitle: crystal structure of glutamate racemase from francisella tularensis2 subsp. tularensis schu s4 in complex with d-glutamate.
101d1ecfa1



not modelled 57.0 23 Fold:PRTase-like
Superfamily:PRTase-like
Family:Phosphoribosyltransferases (PRTases)
102d1c4oa2



not modelled 56.9 8 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
103d1pq4a_



not modelled 56.6 15 Fold:Chelatase-like
Superfamily:"Helical backbone" metal receptor
Family:TroA-like
104c2puwA_



not modelled 56.5 10 PDB header:transferase
Chain: A: PDB Molecule:isomerase domain of glutamine-fructose-6-phosphate
PDBTitle: the crystal structure of isomerase domain of glucosamine-6-phosphate2 synthase from candida albicans
105c2xznB_



not modelled 56.4 17 PDB header:ribosome
Chain: B: PDB Molecule:rps0e;
PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2
106c3dmdA_



not modelled 55.8 17 PDB header:transport protein
Chain: A: PDB Molecule:signal recognition particle receptor;
PDBTitle: structures and conformations in solution of the signal recognition2 particle receptor from the archaeon pyrococcus furiosus
107c2pi2A_



not modelled 55.7 18 PDB header:replication, dna binding protein
Chain: A: PDB Molecule:replication protein a 32 kda subunit;
PDBTitle: full-length replication protein a subunits rpa14 and rpa32
108c3aaxB_



not modelled 55.6 10 PDB header:transferase
Chain: B: PDB Molecule:putative thiosulfate sulfurtransferase;
PDBTitle: crystal structure of probable thiosulfate sulfurtransferase2 cysa3 (rv3117) from mycobacterium tuberculosis: monoclinic3 form
109d1otha2



not modelled 55.4 27 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
110c1y5iA_



not modelled 55.3 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain;
PDBTitle: the crystal structure of the narghi mutant nari-k86a
111c2ph5A_



not modelled 55.2 19 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
112c3rlhA_



not modelled 55.1 23 PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase d lisictox-alphaia1a;
PDBTitle: crystal structure of a class ii phospholipase d from loxosceles2 intermedia venom
113c3eyxB_



not modelled 54.9 24 PDB header:lyase
Chain: B: PDB Molecule:carbonic anhydrase;
PDBTitle: crystal structure of carbonic anhydrase nce103 from2 saccharomyces cerevisiae
114c2yz5B_



not modelled 54.0 21 PDB header:hydrolase
Chain: B: PDB Molecule:histidinol phosphatase;
PDBTitle: histidinol phosphate phosphatase complexed with phosphate
115d1duvg2



not modelled 53.9 18 Fold:ATC-like
Superfamily:Aspartate/ornithine carbamoyltransferase
Family:Aspartate/ornithine carbamoyltransferase
116c3q41B_



not modelled 53.7 12 PDB header:transport protein
Chain: B: PDB Molecule:glutamate [nmda] receptor subunit zeta-1;
PDBTitle: crystal structure of the glun1 n-terminal domain (ntd)
117d1m65a_



not modelled 53.3 28 Fold:7-stranded beta/alpha barrel
Superfamily:PHP domain-like
Family:PHP domain
118c2j17A_



not modelled 53.2 16 PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase yil113w;
PDBTitle: ptyr bound form of sdp-1
119c2w3nA_



not modelled 53.1 29 PDB header:lyase
Chain: A: PDB Molecule:carbonic anhydrase 2;
PDBTitle: structure and inhibition of the co2-sensing carbonic2 anhydrase can2 from the pathogenic fungus cryptococcus3 neoformans
120c3pshA_



not modelled 52.7 10 PDB header:metal transport
Chain: A: PDB Molecule:protein hi_1472;
PDBTitle: classification of a haemophilus influenzae abc transporter hi1470/712 through its cognate molybdate periplasmic binding protein mola (mola3 bound to molybdate)

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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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