Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77374
DateThu Jan 5 12:28:16 GMT 2012
Unique Job IDf80e8aa8888f794b

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1y5iA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain;
PDBTitle: the crystal structure of the narghi mutant nari-k86a
Confidence and coverage
Confidence:100.0% Coverage: 91%
738 residues ( 91% 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.
791 residues ( 98%) 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  MSKNERMVGISRRTLVKSTAIGSLALAAGGFSLPFTLRNAAAAVQQAREKVVWGACSVNC
Secondary structure 
SS confidence 
Disorder  ???????????
???????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GSRCALRLHVKDNEVTWVETDNTGSDEYGNHQVRACLRGRSIRRRINHPDRLNYPMKRVG
Secondary structure 
SS confidence 
Disorder 
?
??
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  KRGEGKFERISWDEALDTIASSLKKTVEQYGNEAVYIQYSSGIVGGNMTRSSPSASAVKR
Secondary structure 
SS confidence 
Disorder  ????
???
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LMNCYGGSLNQYGSYSTAQISCAMPYTYGSNDGNSTTDIENSKLVVMFGNNPAETRMSGG
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  GITYLLEKAREKSNAKMIVIDPRYTDTAAGREDEWLPIRPGTDAALVAGIAWVLINENLV
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  DQPFLDKYCVGYDEKTLPADAPKNGHYKAYILGEGDDKTAKTPQWASQITGIPEDRIIKL
Secondary structure 
SS confidence 
Disorder 
?
??
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  AREIGTAKPAYICQGWGPQRQANGELTARAIAMLPILTGNVGISGGNSGARESTYTITIE
Secondary structure 
SS confidence 
Disorder 
?
?????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  RLPVLDNPVKTSISCFSWTDAIDHGPQMTAIRDGVRGKDKLDVPIKFIWNYAGNTLVNQH
Secondary structure 
SS confidence 
Disorder 
?
?
?
??
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  SDINKTHEILQDESKCEMIVVIENFMTSSAKYADILLPDLMTVEQEDIIPNDYAGNMGYL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  IFLQPVTSEKFERKPIYWILSEVAKRLGPDVYQKFTEGRTQEQWLQHLYAKMLAKDPALP
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  SYDELKKMGIYKRKDPNGHFVAYKAFRDDPEANPLKTPSGKIEIYSSRLAEIARTWELEK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  DEVISPLPVYASTFEGWNSPERRTFPLQLFGFHYKSRTHSTYGNIDLLKAACRQEVWINP
Secondary structure 
SS confidence 
Disorder 
??
??
?
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  IDAQKRGIANGDMVRVFNHRGEVRLPAKVTPRILPGVSAMGQGAWHEANMSGDKIDHGGC
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 
   .........790.........800........
Sequence  VNTLTTLRPSPLAKGNPQHTNLVEIEKI
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 1y5i chain A

3D model

Region: 47 - 808
Aligned: 738
Modelled: 751
Confidence: 100.0%
Identity: 29%
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 1kqg chain A

3D model

Region: 47 - 807
Aligned: 733
Modelled: 758
Confidence: 100.0%
Identity: 24%
PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit;
PDBTitle: formate dehydrogenase n from e. coli

Phyre2

PDB 1tmo chain A

3D model

Region: 47 - 808
Aligned: 717
Modelled: 739
Confidence: 100.0%
Identity: 27%
PDB header:oxidoreductase
Chain: A: PDB Molecule:trimethylamine n-oxide reductase;
PDBTitle: trimethylamine n-oxide reductase from shewanella massilia

Phyre2

PDB 1h5n chain C

3D model

Region: 54 - 808
Aligned: 714
Modelled: 734
Confidence: 100.0%
Identity: 29%
PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air

Phyre2

PDB 1h0h chain A

3D model

Region: 40 - 807
Aligned: 735
Modelled: 761
Confidence: 100.0%
Identity: 24%
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: 52 - 807
Aligned: 682
Modelled: 723
Confidence: 100.0%
Identity: 26%
PDB header:lyase
Chain: A: PDB Molecule:acetylene hydratase ahy;
PDBTitle: acetylene hydratase from pelobacter acetylenicus

Phyre2

PDB 1eu1 chain A

3D model

Region: 54 - 807
Aligned: 714
Modelled: 730
Confidence: 100.0%
Identity: 29%
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: 49 - 808
Aligned: 732
Modelled: 744
Confidence: 100.0%
Identity: 25%
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: 42 - 808
Aligned: 694
Modelled: 733
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: 46 - 807
Aligned: 717
Modelled: 749
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: 47 - 807
Aligned: 703
Modelled: 715
Confidence: 100.0%
Identity: 22%
PDB header:oxidoreductase
Chain: F: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the periplasmic nitrate reductase2 (nap) from escherichia coli

Phyre2

PDB 1ogy chain A

3D model

Region: 49 - 806
Aligned: 707
Modelled: 707
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 2v45 chain A

3D model

Region: 45 - 807
Aligned: 699
Modelled: 726
Confidence: 100.0%
Identity: 23%
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 2iv2 chain X

3D model

Region: 50 - 807
Aligned: 672
Modelled: 704
Confidence: 100.0%
Identity: 23%
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: 43 - 808
Aligned: 690
Modelled: 720
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 1kqf chain A domain 2

3D model

Region: 47 - 741
Aligned: 640
Modelled: 660
Confidence: 100.0%
Identity: 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

Phyre2

PDB 1y5i chain A domain 2

3D model

Region: 47 - 676
Aligned: 604
Modelled: 621
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 1tmo chain A domain 2

3D model

Region: 47 - 673
Aligned: 582
Modelled: 607
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 2jio chain A domain 2

3D model

Region: 48 - 647
Aligned: 562
Modelled: 585
Confidence: 100.0%
Identity: 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

Phyre2

PDB 1dmr chain A domain 2

3D model

Region: 54 - 674
Aligned: 583
Modelled: 607
Confidence: 100.0%
Identity: 27%
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: 8 - 29
Aligned: 22
Modelled: 22
Confidence: 95.1%
Identity: 41%
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: 9 - 34
Aligned: 26
Modelled: 26
Confidence: 91.3%
Identity: 27%
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: 2 - 31
Aligned: 30
Modelled: 30
Confidence: 80.9%
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
c1y5iA_
2
c1kqgA_
3
c1tmoA_
4
c1h5nC_
5
c1h0hA_
6
c2e7zA_
7
c1eu1A_
8
c1vlfQ_
9
c2vpyE_
10
c2ivfA_
11
c2nyaF_
12
c1ogyA_
13
c2v45A_
14
c2iv2X_
15
c1g8jC_
16
d1kqfa2
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d1y5ia2
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d1tmoa2
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d2jioa2
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d1dmra2
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c2pq4B_
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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
1c1y5iA_
100.0 29 PDB header:oxidoreductase
Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain;
PDBTitle: the crystal structure of the narghi mutant nari-k86a
2c1kqgA_
100.0 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit;
PDBTitle: formate dehydrogenase n from e. coli
3c1tmoA_
100.0 27 PDB header:oxidoreductase
Chain: A: PDB Molecule:trimethylamine n-oxide reductase;
PDBTitle: trimethylamine n-oxide reductase from shewanella massilia
4c1h5nC_
100.0 29 PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air
5c1h0hA_
100.0 24 PDB header:dehydrogenase
Chain: A: PDB Molecule:formate dehydrogenase (large subunit);
PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas
6c2e7zA_
100.0 26 PDB header:lyase
Chain: A: PDB Molecule:acetylene hydratase ahy;
PDBTitle: acetylene hydratase from pelobacter acetylenicus
7c1eu1A_
100.0 29 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 25 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 22 PDB header:oxidoreductase
Chain: F: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the periplasmic nitrate reductase2 (nap) from escherichia coli
12c1ogyA_
100.0 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the heterodimeric nitrate reductase2 from rhodobacter sphaeroides
13c2v45A_
100.0 23 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
14c2iv2X_
100.0 23 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
16d1kqfa2
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
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
18d1tmoa2
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
19d2jioa2
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
20d1dmra2
100.0 27 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
21d1vlfm2
not modelled 100.0 23 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
22d1eu1a2
not modelled 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
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 24 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 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
26d1g8ka2
not modelled 100.0 19 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 17 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 16 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
29d1kqfa1
not modelled 100.0 26 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
30d1tmoa1
not modelled 100.0 34 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
31d1dmra1
not modelled 100.0 34 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
32d1eu1a1
not modelled 100.0 36 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
33d1vlfm1
not modelled 100.0 35 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
34d1h0ha1
not modelled 99.9 20 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
35d2jioa1
not modelled 99.9 26 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
36d1ogya1
not modelled 99.9 26 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
37d1g8ka1
not modelled 99.9 17 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
38d1y5ia1
not modelled 99.9 27 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 99.8 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
42d2ihta1
not modelled 96.4 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
43c2pjhB_
not modelled 96.2 13 PDB header:transport protein
Chain: B: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: strctural model of the p97 n domain- npl4 ubd complex
44d1ozha1
not modelled 96.1 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
45d1q6za1
not modelled 96.1 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
46d1e32a1
not modelled 95.3 13 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
47d2ji7a1
not modelled 95.2 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
48d2ez9a1
not modelled 95.1 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
49c2pq4B_
95.1 41 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
50c1cz5A_
not modelled 94.7 14 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)
51d1ybha1
not modelled 94.6 17 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
52c3k35D_
not modelled 94.4 13 PDB header:hydrolase
Chain: D: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: crystal structure of human sirt6
53d2djia1
not modelled 94.3 19 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
54d1zpda1
not modelled 94.0 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
55d1x92a_
not modelled 94.0 12 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
56c2x3yA_
not modelled 93.9 8 PDB header:isomerase
Chain: A: PDB Molecule:phosphoheptose isomerase;
PDBTitle: crystal structure of gmha from burkholderia pseudomallei
57c3pkiF_
not modelled 93.7 13 PDB header:hydrolase
Chain: F: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: human sirt6 crystal structure in complex with adp ribose
58d1cz5a1
not modelled 93.7 15 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
59d1tk9a_
not modelled 93.2 13 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
60d1x94a_
not modelled 93.2 18 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
61d1ovma1
not modelled 93.0 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
62d1t9ba1
not modelled 92.7 11 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
63d1ma3a_
not modelled 92.5 15 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
64c3jwpA_
not modelled 92.5 13 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
65c3hu2C_
not modelled 91.8 13 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
66c1s3sA_
not modelled 91.6 12 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
67d2b4ya1
not modelled 91.6 7 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
68c2e76D_
91.3 27 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
69c3etnD_
not modelled 90.8 13 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
70c3knzA_
not modelled 90.8 16 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
71c3fxaA_
not modelled 90.4 17 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
72c1p84E_
not modelled 89.6 13 PDB header:oxidoreductase
Chain: E: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur
PDBTitle: hdbt inhibited yeast cytochrome bc1 complex
73d1yc5a1
not modelled 89.4 9 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
74c2dwcB_
not modelled 89.3 10 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
75c2yvaB_
not modelled 89.3 11 PDB header:dna binding protein
Chain: B: PDB Molecule:dnaa initiator-associating protein diaa;
PDBTitle: crystal structure of escherichia coli diaa
76c3cf1C_
not modelled 89.2 11 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
77c3euaD_
not modelled 88.3 16 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
78d1pvda1
not modelled 87.6 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
79d1m2ka_
not modelled 87.4 13 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
80d1kjqa2
not modelled 86.6 14 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
81d1s5pa_
not modelled 85.4 12 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
82c2fynO_
not modelled 84.5 29 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
83c1kjjA_
not modelled 84.3 13 PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s
84d1ylea1
not modelled 81.5 23 Fold:Acyl-CoA N-acyltransferases (Nat)
Superfamily:Acyl-CoA N-acyltransferases (Nat)
Family:AstA-like
85c2fyuE_
80.9 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
86d1vima_
not modelled 80.8 14 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
87c2ji6B_
not modelled 80.7 15 PDB header:lyase
Chain: B: PDB Molecule:oxalyl-coa decarboxylase;
PDBTitle: x-ray structure of oxalyl-coa decarboxylase in complex with2 3-deaza-thdp and oxalyl-coa
88c1wlfA_
not modelled 80.7 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
89c2a3nA_
not modelled 79.9 11 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
90d1m3sa_
not modelled 78.5 14 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
91d1qcsa1
not modelled 74.9 19 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
92d1jeoa_
not modelled 74.9 19 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
93c1jscA_
not modelled 74.7 11 PDB header:lyase
Chain: A: PDB Molecule:acetohydroxy-acid synthase;
PDBTitle: crystal structure of the catalytic subunit of yeast2 acetohydroxyacid synthase: a target for herbicidal3 inhibitors
94c3g68A_
not modelled 74.0 15 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
95d1wlfa2
not modelled 73.4 32 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
96c2x7jA_
not modelled 73.1 16 PDB header:transferase
Chain: A: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene
PDBTitle: structure of the menaquinone biosynthesis protein mend from2 bacillus subtilis
97c3q2oB_
not modelled 71.2 18 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase
98c3trjC_
not modelled 70.6 14 PDB header:isomerase
Chain: C: PDB Molecule:phosphoheptose isomerase;
PDBTitle: structure of a phosphoheptose isomerase from francisella tularensis
99c3fkjA_
not modelled 70.4 14 PDB header:isomerase
Chain: A: PDB Molecule:putative phosphosugar isomerases;
PDBTitle: crystal structure of a putative phosphosugar isomerase (stm_0572) from2 salmonella typhimurium lt2 at 2.12 a resolution
100c3orqA_
not modelled 68.0 17 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
101c3m7aA_
not modelled 65.2 38 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
102c3lq1A_
not modelled 65.0 13 PDB header:transferase
Chain: A: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-
PDBTitle: crystal structure of 2-succinyl-6-hydroxy-2,4-cyclohexadiene2 1-carboxylic acid synthase/2-oxoglutarate decarboxylase3 from listeria monocytogenes str. 4b f2365
103c3glsC_
not modelled 64.8 16 PDB header:hydrolase
Chain: C: PDB Molecule:nad-dependent deacetylase sirtuin-3,
PDBTitle: crystal structure of human sirt3
104d1cr5a1
not modelled 64.4 15 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
105c2amlB_
not modelled 63.2 18 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
106c2l66B_
not modelled 62.9 27 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.
107c3iwfA_
not modelled 62.0 16 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
108c1qdnA_
not modelled 59.8 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)
109d1nria_
not modelled 58.7 14 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
110c1nriA_
not modelled 58.7 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein hi0754;
PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae
111d1b25a1
not modelled 56.3 17 Fold:Aldehyde ferredoxin oxidoreductase, C-terminal domains
Superfamily:Aldehyde ferredoxin oxidoreductase, C-terminal domains
Family:Aldehyde ferredoxin oxidoreductase, C-terminal domains
112c3pjyB_
not modelled 55.4 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
113d2vbua1
not modelled 54.7 14 Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin kinase-like
Family:CTP-dependent riboflavin kinase-like
114c3cvjB_
not modelled 53.8 15 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
115c2zj3A_
not modelled 53.0 16 PDB header:transferase
Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate
PDBTitle: isomerase domain of human glucose:fructose-6-phosphate2 amidotransferase
116c3uvzB_
not modelled 52.4 20 PDB header:lyase
Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit;
PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase, atpase2 subunit from burkholderia ambifaria
117d1moqa_
not modelled 49.5 20 Fold:SIS domain
Superfamily:SIS domain
Family:double-SIS domain
118c2xhzC_
not modelled 49.0 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
119c2ev2B_
not modelled 49.0 21 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
120d1d4oa_
not modelled 48.4 21 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Transhydrogenase domain III (dIII)

Binding site prediction 

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

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


Phyre is for academic use only

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