Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP18775
DateWed Jan 25 15:20:41 GMT 2012
Unique Job IDada7ed6672879a0b

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1tmoA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:trimethylamine n-oxide reductase;
PDBTitle: trimethylamine n-oxide reductase from shewanella massilia
Confidence and coverage
Confidence:100.0% Coverage: 88%
716 residues ( 88% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
803 residues ( 99%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKTKIPDAVLAAEVSRRGLVKTTAIGGLAMASSALTLPFSRIAHAVDSAIPTKSDEKVIW
Secondary structure 
SS confidence 
Disorder  ?????????????
?????????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  SACTVNCGSRCPLRMHVVDGEIKYVETDNTGDDNYDGLHQVRACLRGRSMRRRVYNPDRL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  KYPMKRVGARGEGKFERISWEEAYDIIATNMQRLIKEYGNESIYLNYGTGTLGGTMTRSW
Secondary structure 
SS confidence 
Disorder 
?
?????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  PPGNTLVARLMNCCGGYLNHYGDYSSAQIAEGLNYTYGGWADGNSPSDIENSKLVVLFGN
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  NPGETRMSGGGVTYYLEQARQKSNARMIIIDPRYTDTGAGREDEWIPIRPGTDAALVNGL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  AYVMITENLVDQAFLDKYCVGYDEKTLPASAPKNGHYKAYILGEGPDGVAKTPEWASQIT
Secondary structure 
SS confidence 
Disorder 
?
??
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  GVPADKIIKLAREIGSTKPAFISQGWGPQRHANGEIATRAISMLAILTGNVGINGGNSGA
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  REGSYSLPFVRMPTLENPIQTSISMFMWTDAIERGPEMTALRDGVRGKDKLDVPIKMIWN
Secondary structure 
SS confidence 
Disorder 
?
?
?
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  YAGNCLINQHSEINRTHEILQDDKKCELIVVIDCHMTSSAKYADILLPDCTASEQMDFAL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  DASCGNMSYVIFNDQVIKPRFECKTIYEMTSELAKRLGVEQQFTEGRTQEEWMRHLYAQS
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  REAIPELPTFEEFRKQGIFKKRDPQGHHVAYKAFREDPQANPLTTPSGKIEIYSQALADI
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  AATWELPEGDVIDPLPIYTPGFESYQDPLNKQYPLQLTGFHYKSRVHSTYGNVDVLKAAC
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  RQEMWINPLDAQKRGIHNGDKVRIFNDRGEVHIEAKVTPRMMPGVVALGEGAWYDPDAKR
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........790.........800.........810....
Sequence  VDKGGCINVLTTQRPSPLAKGNPSHTNLVQVEKV
Secondary structure 
SS confidence 
Disorder  ?
?
??
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 1tmo chain A

3D model

Region: 54 - 814
Aligned: 716
Modelled: 733
Confidence: 100.0%
Identity: 29%
PDB header:oxidoreductase
Chain: A: PDB Molecule:trimethylamine n-oxide reductase;
PDBTitle: trimethylamine n-oxide reductase from shewanella massilia

Phyre2

PDB 1y5i chain A

3D model

Region: 44 - 814
Aligned: 753
Modelled: 770
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase
Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain;
PDBTitle: the crystal structure of the narghi mutant nari-k86a

Phyre2

PDB 1h5n chain C

3D model

Region: 61 - 814
Aligned: 713
Modelled: 738
Confidence: 100.0%
Identity: 30%
PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air

Phyre2

PDB 1kqg chain A

3D model

Region: 47 - 813
Aligned: 740
Modelled: 760
Confidence: 100.0%
Identity: 23%
PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit;
PDBTitle: formate dehydrogenase n from e. coli

Phyre2

PDB 1h0h chain A

3D model

Region: 48 - 813
Aligned: 732
Modelled: 749
Confidence: 100.0%
Identity: 23%
PDB header:dehydrogenase
Chain: A: PDB Molecule:formate dehydrogenase (large subunit);
PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas

Phyre2

PDB 2e7z chain A

3D model

Region: 59 - 813
Aligned: 683
Modelled: 729
Confidence: 100.0%
Identity: 25%
PDB header:lyase
Chain: A: PDB Molecule:acetylene hydratase ahy;
PDBTitle: acetylene hydratase from pelobacter acetylenicus

Phyre2

PDB 1eu1 chain A

3D model

Region: 61 - 813
Aligned: 711
Modelled: 733
Confidence: 100.0%
Identity: 32%
PDB header:oxidoreductase
Chain: A: PDB Molecule:dimethyl sulfoxide reductase;
PDBTitle: the crystal structure of rhodobacter sphaeroides dimethylsulfoxide2 reductase reveals two distinct molybdenum coordination environments.

Phyre2

PDB 1vlf chain Q

3D model

Region: 57 - 814
Aligned: 730
Modelled: 730
Confidence: 100.0%
Identity: 27%
PDB header:oxidoreductase
Chain: Q: PDB Molecule:pyrogallol hydroxytransferase large subunit;
PDBTitle: crystal structure of pyrogallol-phloroglucinol2 transhydroxylase from pelobacter acidigallici complexed3 with inhibitor 1,2,4,5-tetrahydroxy-benzene

Phyre2

PDB 2vpy chain E

3D model

Region: 49 - 814
Aligned: 693
Modelled: 736
Confidence: 100.0%
Identity: 28%
PDB header:oxidoreductase
Chain: E: PDB Molecule:thiosulfate reductase;
PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp)

Phyre2

PDB 2ivf chain A

3D model

Region: 51 - 813
Aligned: 725
Modelled: 754
Confidence: 100.0%
Identity: 24%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum

Phyre2

PDB 2nya chain F

3D model

Region: 54 - 813
Aligned: 702
Modelled: 714
Confidence: 100.0%
Identity: 23%
PDB header:oxidoreductase
Chain: F: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the periplasmic nitrate reductase2 (nap) from escherichia coli

Phyre2

PDB 2v45 chain A

3D model

Region: 53 - 813
Aligned: 699
Modelled: 733
Confidence: 100.0%
Identity: 22%
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

Phyre2

PDB 1ogy chain A

3D model

Region: 56 - 812
Aligned: 706
Modelled: 706
Confidence: 100.0%
Identity: 21%
PDB header:oxidoreductase
Chain: A: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the heterodimeric nitrate reductase2 from rhodobacter sphaeroides

Phyre2

PDB 2iv2 chain X

3D model

Region: 57 - 813
Aligned: 673
Modelled: 702
Confidence: 100.0%
Identity: 24%
PDB header:oxidoreductase
Chain: X: PDB Molecule:formate dehydrogenase h;
PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli

Phyre2

PDB 1g8j chain C

3D model

Region: 52 - 814
Aligned: 686
Modelled: 712
Confidence: 100.0%
Identity: 18%
PDB header:oxidoreductase
Chain: C: PDB Molecule:arsenite oxidase;
PDBTitle: crystal structure analysis of arsenite oxidase from2 alcaligenes faecalis

Phyre2

PDB 1tmo chain A domain 2

3D model

Region: 54 - 682
Aligned: 584
Modelled: 617
Confidence: 100.0%
Identity: 26%
Fold: Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily: Formate dehydrogenase/DMSO reductase, domains 1-3
Family: Formate dehydrogenase/DMSO reductase, domains 1-3

Phyre2

PDB 1y5i chain A domain 2

3D model

Region: 44 - 684
Aligned: 614
Modelled: 641
Confidence: 100.0%
Identity: 30%
Fold: Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily: Formate dehydrogenase/DMSO reductase, domains 1-3
Family: Formate dehydrogenase/DMSO reductase, domains 1-3

Phyre2

PDB 1dmr chain A domain 2

3D model

Region: 61 - 682
Aligned: 582
Modelled: 613
Confidence: 100.0%
Identity: 28%
Fold: Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily: Formate dehydrogenase/DMSO reductase, domains 1-3
Family: Formate dehydrogenase/DMSO reductase, domains 1-3

Phyre2

PDB 2jio chain A domain 2

3D model

Region: 56 - 658
Aligned: 565
Modelled: 584
Confidence: 100.0%
Identity: 21%
Fold: Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily: Formate dehydrogenase/DMSO reductase, domains 1-3
Family: Formate dehydrogenase/DMSO reductase, domains 1-3

Phyre2

PDB 1kqf chain A domain 2

3D model

Region: 47 - 749
Aligned: 663
Modelled: 674
Confidence: 100.0%
Identity: 20%
Fold: Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily: Formate dehydrogenase/DMSO reductase, domains 1-3
Family: Formate dehydrogenase/DMSO reductase, domains 1-3

Phyre2

PDB 2pq4 chain B

3D model

Region: 12 - 33
Aligned: 22
Modelled: 22
Confidence: 93.3%
Identity: 32%
PDB header:chaperone/oxidoreductase
Chain: B: PDB Molecule:periplasmic nitrate reductase precursor;
PDBTitle: nmr solution structure of napd in complex with napa1-352 signal peptide

Phyre2

PDB 2e76 chain D

3D model

Region: 13 - 56
Aligned: 44
Modelled: 44
Confidence: 92.4%
Identity: 14%
PDB header:photosynthesis
Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus

Phyre2

PDB 2fyu chain E

3D model

Region: 6 - 36
Aligned: 31
Modelled: 31
Confidence: 80.0%
Identity: 10%
PDB header:oxidoreductase
Chain: E: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur subunit,
PDBTitle: crystal structure of bovine heart mitochondrial bc1 with jg1442 inhibitor

Phyre2
1
c1tmoA_
2
c1y5iA_
3
c1h5nC_
4
c1kqgA_
5
c1h0hA_
6
c2e7zA_
7
c1eu1A_
8
c1vlfQ_
9
c2vpyE_
10
c2ivfA_
11
c2nyaF_
12
c2v45A_
13
c1ogyA_
14
c2iv2X_
15
c1g8jC_
16
d1tmoa2
17
d1y5ia2
18
d1dmra2
19
d2jioa2
20
d1kqfa2
21
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c2pq4B_
55
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c2e76D_
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c2fyuE_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1tmoA_
100.0 29 PDB header:oxidoreductase
Chain: A: PDB Molecule:trimethylamine n-oxide reductase;
PDBTitle: trimethylamine n-oxide reductase from shewanella massilia
2c1y5iA_
100.0 28 PDB header:oxidoreductase
Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain;
PDBTitle: the crystal structure of the narghi mutant nari-k86a
3c1h5nC_
100.0 30 PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air
4c1kqgA_
100.0 23 PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit;
PDBTitle: formate dehydrogenase n from e. coli
5c1h0hA_
100.0 23 PDB header:dehydrogenase
Chain: A: PDB Molecule:formate dehydrogenase (large subunit);
PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas
6c2e7zA_
100.0 25 PDB header:lyase
Chain: A: PDB Molecule:acetylene hydratase ahy;
PDBTitle: acetylene hydratase from pelobacter acetylenicus
7c1eu1A_
100.0 32 PDB header:oxidoreductase
Chain: A: PDB Molecule:dimethyl sulfoxide reductase;
PDBTitle: the crystal structure of rhodobacter sphaeroides dimethylsulfoxide2 reductase reveals two distinct molybdenum coordination environments.
8c1vlfQ_
100.0 27 PDB header:oxidoreductase
Chain: Q: PDB Molecule:pyrogallol hydroxytransferase large subunit;
PDBTitle: crystal structure of pyrogallol-phloroglucinol2 transhydroxylase from pelobacter acidigallici complexed3 with inhibitor 1,2,4,5-tetrahydroxy-benzene
9c2vpyE_
100.0 28 PDB header:oxidoreductase
Chain: E: PDB Molecule:thiosulfate reductase;
PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp)
10c2ivfA_
100.0 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum
11c2nyaF_
100.0 23 PDB header:oxidoreductase
Chain: F: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the periplasmic nitrate reductase2 (nap) from escherichia coli
12c2v45A_
100.0 22 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
13c1ogyA_
100.0 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the heterodimeric nitrate reductase2 from rhodobacter sphaeroides
14c2iv2X_
100.0 24 PDB header:oxidoreductase
Chain: X: PDB Molecule:formate dehydrogenase h;
PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli
15c1g8jC_
100.0 18 PDB header:oxidoreductase
Chain: C: PDB Molecule:arsenite oxidase;
PDBTitle: crystal structure analysis of arsenite oxidase from2 alcaligenes faecalis
16d1tmoa2
100.0 26 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
17d1y5ia2
100.0 30 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
18d1dmra2
100.0 28 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
19d2jioa2
100.0 21 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
20d1kqfa2
100.0 20 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
21d1eu1a2
not modelled 100.0 29 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
22d1vlfm2
not modelled 100.0 26 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
23d1h0ha2
not modelled 100.0 22 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
24d2iv2x2
not modelled 100.0 25 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
25d1ogya2
not modelled 100.0 20 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
26d1g8ka2
not modelled 100.0 18 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
27c2fugC_
not modelled 100.0 18 PDB header:oxidoreductase
Chain: C: PDB Molecule:nadh-quinone oxidoreductase chain 3;
PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus
28d2fug32
not modelled 100.0 17 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
29d1tmoa1
not modelled 100.0 36 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
30d1kqfa1
not modelled 100.0 24 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
31d1dmra1
not modelled 100.0 41 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
32d1eu1a1
not modelled 100.0 42 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
33d1vlfm1
not modelled 100.0 38 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
34d1h0ha1
not modelled 100.0 21 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
35d2jioa1
not modelled 100.0 26 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
36d1g8ka1
not modelled 99.9 16 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
37d1ogya1
not modelled 99.9 25 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
38d1y5ia1
not modelled 99.9 25 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
39d2iv2x1
not modelled 99.9 25 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
40c2ki8A_
not modelled 99.9 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase,
PDBTitle: solution nmr structure of tungsten formylmethanofuran2 dehydrogenase subunit d from archaeoglobus fulgidus,3 northeast structural genomics consortium target att7
41d2fug31
not modelled 96.9 20 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
42c2pjhB_
not modelled 96.4 9 PDB header:transport protein
Chain: B: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: strctural model of the p97 n domain- npl4 ubd complex
43d1e32a1
not modelled 95.4 9 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
44d1q6za1
not modelled 95.1 15 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
45c1cz5A_
not modelled 94.8 15 PDB header:hydrolase
Chain: A: PDB Molecule:vcp-like atpase;
PDBTitle: nmr structure of vat-n: the n-terminal domain of vat (vcp-2 like atpase of thermoplasma)
46d2ihta1
not modelled 94.5 15 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
47d1ozha1
not modelled 94.2 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
48c3k35D_
not modelled 94.1 17 PDB header:hydrolase
Chain: D: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: crystal structure of human sirt6
49c3pkiF_
not modelled 94.0 17 PDB header:hydrolase
Chain: F: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: human sirt6 crystal structure in complex with adp ribose
50d1cz5a1
not modelled 94.0 17 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
51d1ybha1
not modelled 94.0 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
52c1s3sA_
not modelled 93.4 8 PDB header:protein binding
Chain: A: PDB Molecule:transitional endoplasmic reticulum atpase (ter
PDBTitle: crystal structure of aaa atpase p97/vcp nd1 in complex with2 p47 c
53d1x94a_
not modelled 93.4 13 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
54c2pq4B_
93.3 32 PDB header:chaperone/oxidoreductase
Chain: B: PDB Molecule:periplasmic nitrate reductase precursor;
PDBTitle: nmr solution structure of napd in complex with napa1-352 signal peptide
55c3jwpA_
not modelled 93.3 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein sir2 homologue;
PDBTitle: crystal structure of plasmodium falciparum sir2a (pf13_0152) in2 complex with amp
56d2ez9a1
not modelled 93.2 17 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
57d1tk9a_
not modelled 93.0 9 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
58c2x3yA_
not modelled 92.9 6 PDB header:isomerase
Chain: A: PDB Molecule:phosphoheptose isomerase;
PDBTitle: crystal structure of gmha from burkholderia pseudomallei
59c3hu2C_
not modelled 92.9 9 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
60c2e76D_
92.4 14 PDB header:photosynthesis
Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus
61d1x92a_
not modelled 92.0 12 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
62d2djia1
not modelled 91.6 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
63d2b4ya1
not modelled 91.4 7 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
64d1ma3a_
not modelled 90.7 15 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
65c3knzA_
not modelled 90.7 14 PDB header:sugar binding protein
Chain: A: PDB Molecule:putative sugar binding protein;
PDBTitle: crystal structure of putative sugar binding protein (np_459565.1) from2 salmonella typhimurium lt2 at 2.50 a resolution
66c3cf1C_
not modelled 90.5 7 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
67c3fxaA_
not modelled 90.2 18 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
68c1p84E_
not modelled 89.8 8 PDB header:oxidoreductase
Chain: E: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur
PDBTitle: hdbt inhibited yeast cytochrome bc1 complex
69c3etnD_
not modelled 89.0 15 PDB header:isomerase
Chain: D: PDB Molecule:putative phosphosugar isomerase involved in capsule
PDBTitle: crystal structure of putative phosphosugar isomerase involved in2 capsule formation (yp_209877.1) from bacteroides fragilis nctc 93433 at 1.70 a resolution
70d1m2ka_
not modelled 89.0 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
71c2yvaB_
not modelled 88.7 10 PDB header:dna binding protein
Chain: B: PDB Molecule:dnaa initiator-associating protein diaa;
PDBTitle: crystal structure of escherichia coli diaa
72d1yc5a1
not modelled 88.7 11 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
73c3euaD_
not modelled 88.5 12 PDB header:isomerase
Chain: D: PDB Molecule:putative fructose-aminoacid-6-phosphate deglycase;
PDBTitle: crystal structure of a putative phosphosugar isomerase (bsu32610) from2 bacillus subtilis at 1.90 a resolution
74c2dwcB_
not modelled 86.5 13 PDB header:transferase
Chain: B: PDB Molecule:433aa long hypothetical phosphoribosylglycinamide formyl
PDBTitle: crystal structure of probable phosphoribosylglycinamide formyl2 transferase from pyrococcus horikoshii ot3 complexed with adp
75c2fynO_
not modelled 86.3 28 PDB header:oxidoreductase
Chain: O: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur
PDBTitle: crystal structure analysis of the double mutant rhodobacter2 sphaeroides bc1 complex
76c1wlfA_
not modelled 86.0 33 PDB header:protein transport
Chain: A: PDB Molecule:peroxisome biogenesis factor 1;
PDBTitle: structure of the n-terminal domain of pex1 aaa-atpase:2 characterization of a putative adaptor-binding domain
77d1zpda1
not modelled 83.1 19 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
78d1wlfa2
not modelled 81.9 32 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
79d1s5pa_
not modelled 81.1 7 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
80d1ylea1
not modelled 80.6 22 Fold:Acyl-CoA N-acyltransferases (Nat)
Superfamily:Acyl-CoA N-acyltransferases (Nat)
Family:AstA-like
81c3g68A_
not modelled 80.2 12 PDB header:isomerase
Chain: A: PDB Molecule:putative phosphosugar isomerase;
PDBTitle: crystal structure of a putative phosphosugar isomerase (cd3275) from2 clostridium difficile 630 at 1.80 a resolution
82c2fyuE_
80.0 10 PDB header:oxidoreductase
Chain: E: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur subunit,
PDBTitle: crystal structure of bovine heart mitochondrial bc1 with jg1442 inhibitor
83c1kjjA_
not modelled 79.8 14 PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s
84d1kjqa2
not modelled 78.2 17 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
85d1ovma1
not modelled 78.2 9 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
86d1qcsa1
not modelled 74.8 19 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
87c1nriA_
not modelled 74.2 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein hi0754;
PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae
88d1nria_
not modelled 74.2 15 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
89d2ji7a1
not modelled 73.5 19 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
90d1cr5a1
not modelled 69.4 15 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
91c3cvjB_
not modelled 67.3 12 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
92d1pvda1
not modelled 66.8 11 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
93c2zj3A_
not modelled 65.9 16 PDB header:transferase
Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate
PDBTitle: isomerase domain of human glucose:fructose-6-phosphate2 amidotransferase
94c3q2oB_
not modelled 65.6 16 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase
95c1jxaA_
not modelled 65.1 19 PDB header:transferase
Chain: A: PDB Molecule:glucosamine 6-phosphate synthase;
PDBTitle: glucosamine 6-phosphate synthase with glucose 6-phosphate
96c3m7aA_
not modelled 65.0 43 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of saro_0823 (yp_496102.1) a protein of2 unknown function from novosphingobium aromaticivorans dsm3 12444 at 1.22 a resolution
97d1moqa_
not modelled 63.7 20 Fold:SIS domain
Superfamily:SIS domain
Family:double-SIS domain
98c3orqA_
not modelled 62.1 21 PDB header:ligase,biosynthetic protein
Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide synthetase;
PDBTitle: crystal structure of n5-carboxyaminoimidazole synthetase from2 staphylococcus aureus complexed with adp
99c3glsC_
not modelled 59.2 16 PDB header:hydrolase
Chain: C: PDB Molecule:nad-dependent deacetylase sirtuin-3,
PDBTitle: crystal structure of human sirt3
100d1mvfd_
not modelled 57.5 26 Fold:Double-split beta-barrel
Superfamily:AbrB/MazE/MraZ-like
Family:Kis/PemI addiction antidote
101c2l66B_
not modelled 57.3 26 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, abrb family;
PDBTitle: the dna-recognition fold of sso7c4 suggests a new member of spovt-abrb2 superfamily from archaea.
102c2a3nA_
not modelled 56.3 10 PDB header:sugar binding protein
Chain: A: PDB Molecule:putative glucosamine-fructose-6-phosphate aminotransferase;
PDBTitle: crystal structure of a putative glucosamine-fructose-6-phosphate2 aminotransferase (stm4540.s) from salmonella typhimurium lt2 at 1.353 a resolution
103c1qdnA_
not modelled 54.9 15 PDB header:fusion protein
Chain: A: PDB Molecule:protein (n-ethylmaleimide sensitive fusion
PDBTitle: amino terminal domain of the n-ethylmaleimide sensitive2 fusion protein (nsf)
104d2vbua1
not modelled 54.5 21 Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin kinase-like
Family:CTP-dependent riboflavin kinase-like
105c3pjyB_
not modelled 54.5 18 PDB header:transcription regulator
Chain: B: PDB Molecule:hypothetical signal peptide protein;
PDBTitle: crystal structure of a putative transcription regulator (r01717) from2 sinorhizobium meliloti 1021 at 1.55 a resolution
106d1vima_
not modelled 54.3 13 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
107c1y6uA_
not modelled 52.6 35 PDB header:dna binding protein
Chain: A: PDB Molecule:excisionase from transposon tn916;
PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases
108c2a8vA_
not modelled 52.2 13 PDB header:protein/rna
Chain: A: PDB Molecule:rna binding domain of rho transcription
PDBTitle: rho transcription termination factor/rna complex
109d1m3sa_
not modelled 51.3 11 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
110d1t9ba1
not modelled 50.7 29 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
111c3shoA_
not modelled 49.4 9 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)
112c1cr5B_
not modelled 48.5 15 PDB header:endocytosis/exocytosis
Chain: B: PDB Molecule:sec18p (residues 22 - 210);
PDBTitle: n-terminal domain of sec18p
113c2ev2B_
not modelled 47.3 16 PDB header:lyase
Chain: B: PDB Molecule:hypothetical protein rv1264/mt1302;
PDBTitle: structure of rv1264n, the regulatory domain of the mycobacterial2 adenylyl cylcase rv1264, at ph 8.5
114d1jeoa_
not modelled 46.7 17 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
115d2b78a1
not modelled 46.6 12 Fold:PUA domain-like
Superfamily:PUA domain-like
Family:Hypothetical RNA methyltransferase domain (HRMD)
116c3trjC_
not modelled 46.3 10 PDB header:isomerase
Chain: C: PDB Molecule:phosphoheptose isomerase;
PDBTitle: structure of a phosphoheptose isomerase from francisella tularensis
117c3iwfA_
not modelled 45.7 17 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator rpir family;
PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
118c2amlB_
not modelled 45.6 12 PDB header:transferase
Chain: B: PDB Molecule:sis domain protein;
PDBTitle: crystal structure of lmo0035 protein (46906266) from listeria2 monocytogenes 4b f2365 at 1.50 a resolution
119d1ueba3
not modelled 44.9 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
120d2grea1
not modelled 43.5 23 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Aminopeptidase/glucanase lid domain
Family:Aminopeptidase/glucanase lid 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
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