Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP33225
DateThu Jan 5 11:51:24 GMT 2012
Unique Job ID0e755538daa7d9dc

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: 92%
783 residues ( 92% 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  MNNNDLFQASRRRFLAQLGGLTVAGMLGPSLLTPRRATAAQAATDAVISKEGILTGSHWG
Secondary structure 
SS confidence 
Disorder  ??????????
??????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  AIRATVKDGRFVAAKPFELDKYPSKMIAGLPDHVHNAARIRYPMVRVDWLRKRHLSDTSQ
Secondary structure 
SS confidence 
Disorder 
?
???????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  RGDNRFVRVSWDEALDMFYEELERVQKTHGPSALLTASGWQSTGMFHNASGMLAKAIALH
Secondary structure 
SS confidence 
Disorder  ???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  GNSVGTGGDYSTGAAQVILPRVVGSMEVYEQQTSWPLVLQNSKTIVLWGSDLLKNQQANW
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  WCPDHDVYEYYAQLKAKVAAGEIEVISIDPVVTSTHEYLGREHVKHIAVNPQTDVPLQLA
Secondary structure 
SS confidence 
Disorder  ???
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  LAHTLYSENLYDKNFLANYCVGFEQFLPYLLGEKDGQPKDAAWAEKLTGIDAETIRGLAR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  QMAANRTQIIAGWCVQRMQHGEQWAWMIVVLAAMLGQIGLPGGGFGFGWHYNGAGTPGRK
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  GVILSGFSGSTSIPPVHDNSDYKGYSSTIPIARFIDAILEPGKVINWNGKSVKLPPLKMC
Secondary structure 
SS confidence 
Disorder 
??
?
??
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  IFAGTNPFHRHQQINRIIEGLRKLETVIAIDNQWTSTCRFADIVLPATTQFERNDLDQYG
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  NHSNRGIIAMKQVVPPQFEARNDFDIFRELCRRFNREEAFTEGLDEMGWLKRIWQEGVQQ
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  GKGRGVHLPAFDDFWNNKEYVEFDHPQMFVRHQAFREDPDLEPLGTPSGLIEIYSKTIAD
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  MNYDDCQGHPMWFEKIERSHGGPGSQKYPLHLQSVHPDFRLHSQLCESETLRQQYTVAGK
Secondary structure 
SS confidence 
Disorder 
???
????
?
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  EPVFINPQDASARGIRNGDVVRVFNARGQVLAGAVVSDRYAPGVARIHEGAWYDPDKGGE
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........790.........800.........810.........820.........830.........840
Sequence  PGALCKYGNPNVLTIDIGTSQLAQATSAHTTLVEIEKYNGTVEQVTAFNGPVEMVAQCEY
Secondary structure 
SS confidence 
Disorder  ??
?
??
?
Disorder confidence 
 
   ........
Sequence  VPASQVKS
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: 44 - 836
Aligned: 783
Modelled: 793
Confidence: 100.0%
Identity: 53%
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: 50 - 839
Aligned: 761
Modelled: 766
Confidence: 100.0%
Identity: 50%
PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air

Phyre2

PDB 1eu1 chain A

3D model

Region: 50 - 832
Aligned: 759
Modelled: 775
Confidence: 100.0%
Identity: 49%
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: 52 - 825
Aligned: 757
Modelled: 765
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 1y5i chain A

3D model

Region: 45 - 819
Aligned: 735
Modelled: 775
Confidence: 100.0%
Identity: 25%
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 2e7z chain A

3D model

Region: 49 - 818
Aligned: 701
Modelled: 748
Confidence: 100.0%
Identity: 21%
PDB header:lyase
Chain: A: PDB Molecule:acetylene hydratase ahy;
PDBTitle: acetylene hydratase from pelobacter acetylenicus

Phyre2

PDB 2ivf chain A

3D model

Region: 45 - 817
Aligned: 713
Modelled: 754
Confidence: 100.0%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum

Phyre2

PDB 1h0h chain A

3D model

Region: 37 - 817
Aligned: 726
Modelled: 748
Confidence: 100.0%
Identity: 20%
PDB header:dehydrogenase
Chain: A: PDB Molecule:formate dehydrogenase (large subunit);
PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas

Phyre2

PDB 2vpy chain E

3D model

Region: 43 - 827
Aligned: 710
Modelled: 761
Confidence: 100.0%
Identity: 22%
PDB header:oxidoreductase
Chain: E: PDB Molecule:thiosulfate reductase;
PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp)

Phyre2

PDB 1kqg chain A

3D model

Region: 44 - 817
Aligned: 719
Modelled: 719
Confidence: 100.0%
Identity: 20%
PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit;
PDBTitle: formate dehydrogenase n from e. coli

Phyre2

PDB 2nya chain F

3D model

Region: 48 - 817
Aligned: 699
Modelled: 729
Confidence: 100.0%
Identity: 20%
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: 48 - 816
Aligned: 697
Modelled: 729
Confidence: 100.0%
Identity: 20%
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: 40 - 817
Aligned: 701
Modelled: 731
Confidence: 100.0%
Identity: 21%
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 1tmo chain A domain 2

3D model

Region: 44 - 675
Aligned: 622
Modelled: 632
Confidence: 100.0%
Identity: 49%
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: 50 - 676
Aligned: 618
Modelled: 627
Confidence: 100.0%
Identity: 49%
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 2iv2 chain X

3D model

Region: 48 - 774
Aligned: 644
Modelled: 698
Confidence: 100.0%
Identity: 21%
PDB header:oxidoreductase
Chain: X: PDB Molecule:formate dehydrogenase h;
PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli

Phyre2

PDB 1eu1 chain A domain 2

3D model

Region: 51 - 675
Aligned: 604
Modelled: 620
Confidence: 100.0%
Identity: 47%
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 1g8j chain C

3D model

Region: 42 - 832
Aligned: 712
Modelled: 731
Confidence: 100.0%
Identity: 14%
PDB header:oxidoreductase
Chain: C: PDB Molecule:arsenite oxidase;
PDBTitle: crystal structure analysis of arsenite oxidase from2 alcaligenes faecalis

Phyre2

PDB 1vlf chain M domain 2

3D model

Region: 51 - 692
Aligned: 607
Modelled: 642
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 1y5i chain A domain 2

3D model

Region: 45 - 676
Aligned: 594
Modelled: 632
Confidence: 100.0%
Identity: 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

Phyre2

PDB 2pq4 chain B

3D model

Region: 7 - 37
Aligned: 31
Modelled: 31
Confidence: 93.7%
Identity: 29%
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
1
c1tmoA_
2
c1h5nC_
3
c1eu1A_
4
c1vlfQ_
5
c1y5iA_
6
c2e7zA_
7
c2ivfA_
8
c1h0hA_
9
c2vpyE_
10
c1kqgA_
11
c2nyaF_
12
c1ogyA_
13
c2v45A_
14
d1tmoa2
15
d1dmra2
16
c2iv2X_
17
d1eu1a2
18
c1g8jC_
19
d1vlfm2
20
d1y5ia2
21
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c2pq4B_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1tmoA_
100.0 53 PDB header:oxidoreductase
Chain: A: PDB Molecule:trimethylamine n-oxide reductase;
PDBTitle: trimethylamine n-oxide reductase from shewanella massilia
2c1h5nC_
100.0 50 PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air
3c1eu1A_
100.0 49 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.
4c1vlfQ_
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
5c1y5iA_
100.0 25 PDB header:oxidoreductase
Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain;
PDBTitle: the crystal structure of the narghi mutant nari-k86a
6c2e7zA_
100.0 21 PDB header:lyase
Chain: A: PDB Molecule:acetylene hydratase ahy;
PDBTitle: acetylene hydratase from pelobacter acetylenicus
7c2ivfA_
100.0 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum
8c1h0hA_
100.0 20 PDB header:dehydrogenase
Chain: A: PDB Molecule:formate dehydrogenase (large subunit);
PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas
9c2vpyE_
100.0 22 PDB header:oxidoreductase
Chain: E: PDB Molecule:thiosulfate reductase;
PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp)
10c1kqgA_
100.0 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit;
PDBTitle: formate dehydrogenase n from e. coli
11c2nyaF_
100.0 20 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 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:periplasmic nitrate reductase;
PDBTitle: crystal structure of the heterodimeric nitrate reductase2 from rhodobacter sphaeroides
13c2v45A_
100.0 21 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
14d1tmoa2
100.0 49 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
15d1dmra2
100.0 49 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
16c2iv2X_
100.0 21 PDB header:oxidoreductase
Chain: X: PDB Molecule:formate dehydrogenase h;
PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli
17d1eu1a2
100.0 47 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3
Family:Formate dehydrogenase/DMSO reductase, domains 1-3
18c1g8jC_
100.0 14 PDB header:oxidoreductase
Chain: C: PDB Molecule:arsenite oxidase;
PDBTitle: crystal structure analysis of arsenite oxidase from2 alcaligenes faecalis
19d1vlfm2
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
20d1y5ia2
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
21d1kqfa2
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
22d2jioa2
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
23d1h0ha2
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
24d2iv2x2
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
25d1ogya2
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
26d1g8ka2
not modelled 100.0 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
27c2fugC_
not modelled 100.0 15 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 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
29d1tmoa1
not modelled 100.0 64 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
30d1eu1a1
not modelled 100.0 54 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
31d1dmra1
not modelled 100.0 51 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
32d1vlfm1
not modelled 100.0 32 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
33d1kqfa1
not modelled 100.0 24 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
34d1h0ha1
not modelled 100.0 16 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
35d1y5ia1
not modelled 100.0 24 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
36d2jioa1
not modelled 100.0 27 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
37d1ogya1
not modelled 99.9 23 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
38d1g8ka1
not modelled 99.9 19 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
39c2ki8A_
not modelled 99.9 23 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
40d2iv2x1
not modelled 99.9 26 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
41d2fug31
not modelled 96.7 24 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
42c2pjhB_
not modelled 96.6 13 PDB header:transport protein
Chain: B: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: strctural model of the p97 n domain- npl4 ubd complex
43d1ozha1
not modelled 96.4 15 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
44d2ez9a1
not modelled 96.4 15 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
45d1e32a1
not modelled 95.8 13 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
46d1tk9a_
not modelled 95.8 11 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
47d1zpda1
not modelled 95.7 10 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
48c1cz5A_
not modelled 95.6 20 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)
49d2djia1
not modelled 95.5 10 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
50d1ovma1
not modelled 95.3 12 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
51d2ji7a1
not modelled 95.2 12 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
52d1x92a_
not modelled 95.1 10 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
53d2ihta1
not modelled 95.1 17 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
54d1cz5a1
not modelled 95.0 22 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
55c3knzA_
not modelled 94.5 11 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
56c3k35D_
not modelled 94.3 14 PDB header:hydrolase
Chain: D: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: crystal structure of human sirt6
57d1q6za1
not modelled 94.2 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
58c2x3yA_
not modelled 94.1 15 PDB header:isomerase
Chain: A: PDB Molecule:phosphoheptose isomerase;
PDBTitle: crystal structure of gmha from burkholderia pseudomallei
59c3pkiF_
not modelled 94.1 14 PDB header:hydrolase
Chain: F: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: human sirt6 crystal structure in complex with adp ribose
60d1ybha1
not modelled 93.9 16 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
61c2pq4B_
93.7 29 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
62c3hu2C_
not modelled 93.4 12 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97 n-d1 r86a mutant in complex with atpgs
63c1s3sA_
not modelled 93.3 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
64c3euaD_
not modelled 92.0 14 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
65d2b4ya1
not modelled 91.6 18 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
66c3cvjB_
not modelled 91.5 10 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
67c3cf1C_
not modelled 91.3 13 PDB header:transport protein
Chain: C: PDB Molecule:transitional endoplasmic reticulum atpase;
PDBTitle: structure of p97/vcp in complex with adp/adp.alfx
68d1t9ba1
not modelled 90.8 14 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
69d1ma3a_
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
70c2yvaB_
not modelled 90.6 11 PDB header:dna binding protein
Chain: B: PDB Molecule:dnaa initiator-associating protein diaa;
PDBTitle: crystal structure of escherichia coli diaa
71c3jwpA_
not modelled 89.3 9 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
72c3fxaA_
not modelled 89.3 16 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
73c1jxaA_
not modelled 88.7 18 PDB header:transferase
Chain: A: PDB Molecule:glucosamine 6-phosphate synthase;
PDBTitle: glucosamine 6-phosphate synthase with glucose 6-phosphate
74c2fynO_
not modelled 88.1 17 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
75c3g68A_
not modelled 88.0 8 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
76d1s5pa_
not modelled 87.8 10 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
77d1m2ka_
not modelled 87.8 17 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
78c2a3nA_
not modelled 87.8 15 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
79c2e76D_
not modelled 87.3 33 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
80d1pvda1
not modelled 87.2 13 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Pyruvate oxidase and decarboxylase, middle domain
81d1yc5a1
not modelled 87.0 13 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
82c3etnD_
not modelled 86.8 14 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
83d1x94a_
not modelled 86.3 10 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
84c1p84E_
not modelled 86.2 7 PDB header:oxidoreductase
Chain: E: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur
PDBTitle: hdbt inhibited yeast cytochrome bc1 complex
85c2x7jA_
not modelled 85.8 8 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
86c1wlfA_
not modelled 85.6 26 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
87c3fkjA_
not modelled 84.0 10 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
88c2zj3A_
not modelled 83.6 12 PDB header:transferase
Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate
PDBTitle: isomerase domain of human glucose:fructose-6-phosphate2 amidotransferase
89d1ylea1
not modelled 82.8 33 Fold:Acyl-CoA N-acyltransferases (Nat)
Superfamily:Acyl-CoA N-acyltransferases (Nat)
Family:AstA-like
90d1moqa_
not modelled 81.7 20 Fold:SIS domain
Superfamily:SIS domain
Family:double-SIS domain
91d1nria_
not modelled 81.5 13 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
92c1nriA_
not modelled 81.5 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein hi0754;
PDBTitle: crystal structure of putative phosphosugar isomerase hi0754 from2 haemophilus influenzae
93c2vbiF_
not modelled 81.1 15 PDB header:lyase
Chain: F: PDB Molecule:pyruvate decarboxylase;
PDBTitle: holostructure of pyruvate decarboxylase from acetobacter2 pasteurianus
94c3glsC_
not modelled 80.9 10 PDB header:hydrolase
Chain: C: PDB Molecule:nad-dependent deacetylase sirtuin-3,
PDBTitle: crystal structure of human sirt3
95c3hbaA_
not modelled 79.2 8 PDB header:isomerase
Chain: A: PDB Molecule:putative phosphosugar isomerase;
PDBTitle: crystal structure of a putative phosphosugar isomerase (sden_2705)2 from shewanella denitrificans os217 at 2.00 a resolution
96c2fyuE_
not modelled 78.7 14 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
97c2ev2B_
not modelled 76.5 14 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
98d1wlfa2
not modelled 76.4 27 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
99c2vbgB_
not modelled 76.3 14 PDB header:lyase
Chain: B: PDB Molecule:branched-chain alpha-ketoacid decarboxylase;
PDBTitle: the complex structure of the branched-chain keto acid2 decarboxylase (kdca) from lactococcus lactis with 2r-1-3 hydroxyethyl-deazathdp
100c1zpdA_
not modelled 75.7 10 PDB header:alcohol fermentation
Chain: A: PDB Molecule:pyruvate decarboxylase;
PDBTitle: pyruvate decarboxylase from zymomonas mobilis
101d1cr5a1
not modelled 75.0 15 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
102d1qcsa1
not modelled 74.6 14 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
103c2yujA_
not modelled 72.7 21 PDB header:protein binding
Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like;
PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1
104d1jeoa_
not modelled 72.6 14 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
105c3lq1A_
not modelled 71.6 10 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
106d1m3sa_
not modelled 71.5 17 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
107c2djiA_
not modelled 71.4 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate oxidase;
PDBTitle: crystal structure of pyruvate oxidase from aerococcus2 viridans containing fad
108c1zc1A_
not modelled 69.1 20 PDB header:protein turnover
Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1;
PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites
109c2l66B_
not modelled 67.3 17 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.
110c3m7aA_
not modelled 67.2 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
111c1ovmC_
not modelled 67.1 12 PDB header:lyase
Chain: C: PDB Molecule:indole-3-pyruvate decarboxylase;
PDBTitle: crystal structure of indolepyruvate decarboxylase from2 enterobacter cloacae
112c3tbfA_
not modelled 66.9 14 PDB header:transferase
Chain: A: PDB Molecule:glucosamine--fructose-6-phosphate aminotransferase
PDBTitle: c-terminal domain of glucosamine-fructose-6-phosphate aminotransferase2 from francisella tularensis.
113c2panF_
not modelled 63.9 13 PDB header:lyase
Chain: F: PDB Molecule:glyoxylate carboligase;
PDBTitle: crystal structure of e. coli glyoxylate carboligase
114d1vima_
not modelled 63.5 15 Fold:SIS domain
Superfamily:SIS domain
Family:mono-SIS domain
115c1qdnA_
not modelled 62.2 14 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)
116c1y6uA_
not modelled 61.9 24 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
117c1ozhD_
not modelled 60.2 14 PDB header:lyase
Chain: D: PDB Molecule:acetolactate synthase, catabolic;
PDBTitle: the crystal structure of klebsiella pneumoniae acetolactate2 synthase with enzyme-bound cofactor and with an unusual3 intermediate.
118c2dwcB_
not modelled 58.7 14 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
119c3pjyB_
not modelled 57.6 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
120d1q1aa_
not modelled 57.2 9 Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators

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