Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP06149
DateThu Jan 5 10:59:07 GMT 2012
Unique Job ID242b307aa24716c0

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1f0xA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:d-lactate dehydrogenase;
PDBTitle: crystal structure of d-lactate dehydrogenase, a peripheral2 membrane respiratory enzyme.
Confidence and coverage
Confidence:100.0% Coverage: 87%
499 residues ( 87% 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  MSSMTTTDNKAFLNELARLVGSSHLLTDPAKTARYRKGFRSGQGDALAVVFPGSLLELWR
Secondary structure 
SS confidence 
Disorder  ?????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  VLKACVTADKIILMQAANTGLTEGSTPNGNDYDRDVVIISTLRLDKLHVLGKGEQVLAYP
Secondary structure 
SS confidence 
Disorder 
???
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  GTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFARIN
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  EDGKLTLVNHLGIDLGETPEQILSKLDDDRIKDDDVRHDGRHAHDYDYVHRVRDIEADTP
Secondary structure 
SS confidence 
Disorder 
?
?
?
??
?
?
???
???
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  ARYNADPDRLFESSGCAGKLAVFAVRLDTFEAEKNQQVFYIGTNQPEVLTEIRRHILANF
Secondary structure 
SS confidence 
Disorder 
?
?
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  ENLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFNLKGRTDAMLEKVKFFRPH
Secondary structure 
SS confidence 
Disorder  ??
?
?
????
??
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  FTDRAMQKFGHLFPSHLPPRMKNWRDKYEHHLLLKMAGDGVGEAKSWLVDYFKQAEGDFF
Secondary structure 
SS confidence 
Disorder 
?
???
??
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  VCTPEEGSKAFLHRFAAAGAAIRYQAVHSDEVEDILALDIALRRNDTEWYEHLPPEIDSQ
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  LVHKLYYGHFMCYVFHQDYIVKKGVDVHALKEQMLELLQQRGAQYPAEHNVGHLYKAPET
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........550.........560.........570.
Sequence  LQKFYRENDPTNSMNPGIGKTSKRKNWQEVE
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 1f0x chain A

3D model

Region: 9 - 567
Aligned: 499
Modelled: 502
Confidence: 100.0%
Identity: 98%
PDB header:oxidoreductase
Chain: A: PDB Molecule:d-lactate dehydrogenase;
PDBTitle: crystal structure of d-lactate dehydrogenase, a peripheral2 membrane respiratory enzyme.

Phyre2

PDB 1ahu chain B

3D model

Region: 2 - 570
Aligned: 486
Modelled: 494
Confidence: 100.0%
Identity: 12%
PDB header:flavoenzyme
Chain: B: PDB Molecule:vanillyl-alcohol oxidase;
PDBTitle: structure of the octameric flavoenzyme vanillyl-alcohol2 oxidase in complex with p-cresol

Phyre2

PDB 2uuv chain C

3D model

Region: 9 - 556
Aligned: 402
Modelled: 413
Confidence: 100.0%
Identity: 15%
PDB header:transferase
Chain: C: PDB Molecule:alkyldihydroxyacetonephosphate synthase;
PDBTitle: alkyldihydroxyacetonephosphate synthase in p1

Phyre2

PDB 3pm9 chain A

3D model

Region: 7 - 559
Aligned: 443
Modelled: 460
Confidence: 100.0%
Identity: 20%
PDB header:oxidoreductase
Chain: A: PDB Molecule:putative oxidoreductase;
PDBTitle: crystal structure of a putative dehydrogenase (rpa1076) from2 rhodopseudomonas palustris cga009 at 2.57 a resolution

Phyre2

PDB 1wve chain B

3D model

Region: 2 - 567
Aligned: 482
Modelled: 490
Confidence: 100.0%
Identity: 12%
PDB header:oxidoreductase
Chain: B: PDB Molecule:4-cresol dehydrogenase [hydroxylating]
PDBTitle: p-cresol methylhydroxylase: alteration of the structure of2 the flavoprotein subunit upon its binding to the3 cytochrome subunit

Phyre2

PDB 1f0x chain A domain 2

3D model

Region: 9 - 272
Aligned: 264
Modelled: 264
Confidence: 100.0%
Identity: 100%
Fold: FAD-binding/transporter-associated domain-like
Superfamily: FAD-binding/transporter-associated domain-like
Family: FAD-linked oxidases, N-terminal domain

Phyre2

PDB 3bw7 chain A

3D model

Region: 14 - 562
Aligned: 450
Modelled: 456
Confidence: 100.0%
Identity: 15%
PDB header:oxidoreductase
Chain: A: PDB Molecule:cytokinin dehydrogenase 1;
PDBTitle: maize cytokinin oxidase/dehydrogenase complexed with the allenic2 cytokinin analog ha-1

Phyre2

PDB 2exr chain A

3D model

Region: 22 - 564
Aligned: 445
Modelled: 449
Confidence: 100.0%
Identity: 11%
PDB header:oxidoreductase
Chain: A: PDB Molecule:cytokinin dehydrogenase 7;
PDBTitle: x-ray structure of cytokinin oxidase/dehydrogenase (ckx)2 from arabidopsis thaliana at5g21482

Phyre2

PDB 1zr6 chain A

3D model

Region: 10 - 563
Aligned: 420
Modelled: 426
Confidence: 100.0%
Identity: 14%
PDB header:oxidoreductase
Chain: A: PDB Molecule:glucooligosaccharide oxidase;
PDBTitle: the crystal structure of an acremonium strictum glucooligosaccharide2 oxidase reveals a novel flavinylation

Phyre2

PDB 3fwa chain A

3D model

Region: 12 - 567
Aligned: 430
Modelled: 439
Confidence: 100.0%
Identity: 17%
PDB header:flavoprotein
Chain: A: PDB Molecule:reticuline oxidase;
PDBTitle: structure of berberine bridge enzyme, c166a variant in complex with2 (s)-reticuline

Phyre2

PDB 2bvf chain A

3D model

Region: 22 - 564
Aligned: 407
Modelled: 420
Confidence: 100.0%
Identity: 13%
PDB header:oxidase
Chain: A: PDB Molecule:6-hydroxy-d-nicotine oxidase;
PDBTitle: crystal structure of 6-hydoxy-d-nicotine oxidase from2 arthrobacter nicotinovorans. crystal form 3 (p1)

Phyre2

PDB 3d2h chain A

3D model

Region: 12 - 568
Aligned: 431
Modelled: 440
Confidence: 100.0%
Identity: 17%
PDB header:oxidoreductase
Chain: A: PDB Molecule:berberine bridge-forming enzyme;
PDBTitle: structure of berberine bridge enzyme from eschscholzia californica,2 monoclinic crystal form

Phyre2

PDB 2ipi chain D

3D model

Region: 20 - 563
Aligned: 436
Modelled: 463
Confidence: 100.0%
Identity: 12%
PDB header:oxidoreductase
Chain: D: PDB Molecule:aclacinomycin oxidoreductase (aknox);
PDBTitle: crystal structure of aclacinomycin oxidoreductase

Phyre2

PDB 1f0x chain A domain 1

3D model

Region: 274 - 567
Aligned: 237
Modelled: 237
Confidence: 100.0%
Identity: 100%
Fold: Ferredoxin-like
Superfamily: FAD-linked oxidases, C-terminal domain
Family: D-lactate dehydrogenase

Phyre2

PDB 3pop chain D

3D model

Region: 27 - 557
Aligned: 414
Modelled: 435
Confidence: 100.0%
Identity: 13%
PDB header:oxidoreductase
Chain: D: PDB Molecule:gilr oxidase;
PDBTitle: the crystal structure of gilr, an oxidoreductase that catalyzes the2 terminal step of gilvocarcin biosynthesis

Phyre2

PDB 2wdw chain B

3D model

Region: 27 - 563
Aligned: 417
Modelled: 448
Confidence: 100.0%
Identity: 13%
PDB header:oxidoreductase
Chain: B: PDB Molecule:putative hexose oxidase;
PDBTitle: the native crystal structure of the primary hexose oxidase (2 dbv29) in antibiotic a40926 biosynthesis

Phyre2

PDB 1wvf chain A domain 2

3D model

Region: 2 - 273
Aligned: 228
Modelled: 233
Confidence: 100.0%
Identity: 12%
Fold: FAD-binding/transporter-associated domain-like
Superfamily: FAD-binding/transporter-associated domain-like
Family: FAD-linked oxidases, N-terminal domain

Phyre2

PDB 1e8g chain A domain 2

3D model

Region: 2 - 273
Aligned: 230
Modelled: 234
Confidence: 100.0%
Identity: 12%
Fold: FAD-binding/transporter-associated domain-like
Superfamily: FAD-binding/transporter-associated domain-like
Family: FAD-linked oxidases, N-terminal domain

Phyre2

PDB 2y3r chain C

3D model

Region: 25 - 563
Aligned: 438
Modelled: 456
Confidence: 100.0%
Identity: 13%
PDB header:oxidoreductase
Chain: C: PDB Molecule:taml;
PDBTitle: structure of the tirandamycin-bound fad-dependent2 tirandamycin oxidase taml in p21 space group

Phyre2

PDB 2vfv chain A

3D model

Region: 35 - 556
Aligned: 382
Modelled: 390
Confidence: 100.0%
Identity: 17%
PDB header:oxidoreductase
Chain: A: PDB Molecule:xylitol oxidase;
PDBTitle: alditol oxidase from streptomyces coelicolor a3(2): complex2 with sulphite

Phyre2
1
c1f0xA_
2
c1ahuB_
3
c2uuvC_
4
c3pm9A_
5
c1wveB_
6
d1f0xa2
7
c3bw7A_
8
c2exrA_
9
c1zr6A_
10
c3fwaA_
11
c2bvfA_
12
c3d2hA_
13
c2ipiD_
14
d1f0xa1
15
c3popD_
16
c2wdwB_
17
d1wvfa2
18
d1e8ga2
19
c2y3rC_
20
c2vfvA_
21
22
23
24
25
26
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1f0xA_
100.0 98 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-lactate dehydrogenase;
PDBTitle: crystal structure of d-lactate dehydrogenase, a peripheral2 membrane respiratory enzyme.
2c1ahuB_
100.0 12 PDB header:flavoenzyme
Chain: B: PDB Molecule:vanillyl-alcohol oxidase;
PDBTitle: structure of the octameric flavoenzyme vanillyl-alcohol2 oxidase in complex with p-cresol
3c2uuvC_
100.0 15 PDB header:transferase
Chain: C: PDB Molecule:alkyldihydroxyacetonephosphate synthase;
PDBTitle: alkyldihydroxyacetonephosphate synthase in p1
4c3pm9A_
100.0 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:putative oxidoreductase;
PDBTitle: crystal structure of a putative dehydrogenase (rpa1076) from2 rhodopseudomonas palustris cga009 at 2.57 a resolution
5c1wveB_
100.0 12 PDB header:oxidoreductase
Chain: B: PDB Molecule:4-cresol dehydrogenase [hydroxylating]
PDBTitle: p-cresol methylhydroxylase: alteration of the structure of2 the flavoprotein subunit upon its binding to the3 cytochrome subunit
6d1f0xa2
100.0 100 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:FAD-linked oxidases, N-terminal domain
7c3bw7A_
100.0 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:cytokinin dehydrogenase 1;
PDBTitle: maize cytokinin oxidase/dehydrogenase complexed with the allenic2 cytokinin analog ha-1
8c2exrA_
100.0 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:cytokinin dehydrogenase 7;
PDBTitle: x-ray structure of cytokinin oxidase/dehydrogenase (ckx)2 from arabidopsis thaliana at5g21482
9c1zr6A_
100.0 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:glucooligosaccharide oxidase;
PDBTitle: the crystal structure of an acremonium strictum glucooligosaccharide2 oxidase reveals a novel flavinylation
10c3fwaA_
100.0 17 PDB header:flavoprotein
Chain: A: PDB Molecule:reticuline oxidase;
PDBTitle: structure of berberine bridge enzyme, c166a variant in complex with2 (s)-reticuline
11c2bvfA_
100.0 13 PDB header:oxidase
Chain: A: PDB Molecule:6-hydroxy-d-nicotine oxidase;
PDBTitle: crystal structure of 6-hydoxy-d-nicotine oxidase from2 arthrobacter nicotinovorans. crystal form 3 (p1)
12c3d2hA_
100.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:berberine bridge-forming enzyme;
PDBTitle: structure of berberine bridge enzyme from eschscholzia californica,2 monoclinic crystal form
13c2ipiD_
100.0 12 PDB header:oxidoreductase
Chain: D: PDB Molecule:aclacinomycin oxidoreductase (aknox);
PDBTitle: crystal structure of aclacinomycin oxidoreductase
14d1f0xa1
100.0 100 Fold:Ferredoxin-like
Superfamily:FAD-linked oxidases, C-terminal domain
Family:D-lactate dehydrogenase
15c3popD_
100.0 13 PDB header:oxidoreductase
Chain: D: PDB Molecule:gilr oxidase;
PDBTitle: the crystal structure of gilr, an oxidoreductase that catalyzes the2 terminal step of gilvocarcin biosynthesis
16c2wdwB_
100.0 13 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative hexose oxidase;
PDBTitle: the native crystal structure of the primary hexose oxidase (2 dbv29) in antibiotic a40926 biosynthesis
17d1wvfa2
100.0 12 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:FAD-linked oxidases, N-terminal domain
18d1e8ga2
100.0 12 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:FAD-linked oxidases, N-terminal domain
19c2y3rC_
100.0 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:taml;
PDBTitle: structure of the tirandamycin-bound fad-dependent2 tirandamycin oxidase taml in p21 space group
20c2vfvA_
100.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:xylitol oxidase;
PDBTitle: alditol oxidase from streptomyces coelicolor a3(2): complex2 with sulphite
21c1i19B_
not modelled 100.0 11 PDB header:oxidoreductase
Chain: B: PDB Molecule:cholesterol oxidase;
PDBTitle: crystal structure of cholesterol oxidase from b.sterolicum
22d1w1oa2
not modelled 100.0 21 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:FAD-linked oxidases, N-terminal domain
23c3js8A_
not modelled 100.0 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:cholesterol oxidase;
PDBTitle: solvent-stable cholesterol oxidase
24d1hska1
not modelled 100.0 16 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain
25d2i0ka2
not modelled 100.0 16 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:FAD-linked oxidases, N-terminal domain
26d1e8ga1
not modelled 100.0 11 Fold:Ferredoxin-like
Superfamily:FAD-linked oxidases, C-terminal domain
Family:Vanillyl-alcohol oxidase-like
27d1uxya1
not modelled 100.0 13 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain
28c1hskA_
not modelled 100.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:udp-n-acetylenolpyruvoylglucosamine reductase;
PDBTitle: crystal structure of s. aureus murb
29d1wvfa1
not modelled 100.0 12 Fold:Ferredoxin-like
Superfamily:FAD-linked oxidases, C-terminal domain
Family:Vanillyl-alcohol oxidase-like
30c2yvsA_
not modelled 99.9 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:glycolate oxidase subunit glce;
PDBTitle: crystal structure of glycolate oxidase subunit glce from thermus2 thermophilus hb8
31c1mbbA_
not modelled 99.9 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:uridine diphospho-n-acetylenolpyruvylglucosamine
PDBTitle: oxidoreductase
32c3i99A_
not modelled 99.9 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:udp-n-acetylenolpyruvoylglucosamine reductase;
PDBTitle: the crystal structure of the udp-n-acetylenolpyruvoylglucosamine2 reductase from the vibrio cholerae o1 biovar tor
33c2gquA_
not modelled 99.7 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:udp-n-acetylenolpyruvylglucosamine reductase;
PDBTitle: crystal structure of udp-n-acetylenolpyruvylglucosamine2 reductase (murb) from thermus caldophilus
34d1ffvc2
not modelled 97.7 17 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
35d3b9jb2
not modelled 97.6 19 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
36c1n62C_
not modelled 97.5 15 PDB header:oxidoreductase
Chain: C: PDB Molecule:carbon monoxide dehydrogenase medium chain;
PDBTitle: crystal structure of the mo,cu-co dehydrogenase (codh), n-2 butylisocyanide-bound state
37c1t3qF_
not modelled 97.5 14 PDB header:oxidoreductase
Chain: F: PDB Molecule:quinoline 2-oxidoreductase medium subunit;
PDBTitle: crystal structure of quinoline 2-oxidoreductase from pseudomonas2 putida 86
38c1ffuF_
not modelled 97.5 16 PDB header:hydrolase
Chain: F: PDB Molecule:cutm, flavoprotein of carbon monoxide
PDBTitle: carbon monoxide dehydrogenase from hydrogenophaga2 pseudoflava which lacks the mo-pyranopterin moiety of the3 molybdenum cofactor
39d1n62c2
not modelled 97.5 15 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
40c3hrdC_
not modelled 97.5 18 PDB header:oxidoreductase
Chain: C: PDB Molecule:nicotinate dehydrogenase fad-subunit;
PDBTitle: crystal structure of nicotinate dehydrogenase
41d1v97a6
not modelled 97.4 21 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
42d1t3qc2
not modelled 97.4 14 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
43c3etrM_
not modelled 97.3 20 PDB header:oxidoreductase
Chain: M: PDB Molecule:xanthine dehydrogenase/oxidase;
PDBTitle: crystal structure of xanthine oxidase in complex with2 lumazine
44c3b9jJ_
not modelled 97.3 20 PDB header:oxidoreductase
Chain: J: PDB Molecule:xanthine oxidase;
PDBTitle: structure of xanthine oxidase with 2-hydroxy-6-methylpurine
45c2w3rG_
not modelled 97.2 16 PDB header:oxidoreductase
Chain: G: PDB Molecule:xanthine dehydrogenase;
PDBTitle: crystal structure of xanthine dehydrogenase (desulfo form)2 from rhodobacter capsulatus in complex with hypoxanthine
46d1jroa4
not modelled 97.2 17 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
47c1rm6E_
not modelled 97.1 16 PDB header:oxidoreductase
Chain: E: PDB Molecule:4-hydroxybenzoyl-coa reductase beta subunit;
PDBTitle: structure of 4-hydroxybenzoyl-coa reductase from thauera2 aromatica
48d1rm6b2
not modelled 96.7 18 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CO dehydrogenase flavoprotein N-terminal domain-like
49c1wygA_
not modelled 96.7 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:xanthine dehydrogenase/oxidase;
PDBTitle: crystal structure of a rat xanthine dehydrogenase triple mutant2 (c535a, c992r and c1324s)
50d1w1oa1
not modelled 96.3 15 Fold:Ferredoxin-like
Superfamily:FAD-linked oxidases, C-terminal domain
Family:Cytokinin dehydrogenase 1
51c3dedB_
not modelled 78.6 13 PDB header:membrane protein
Chain: B: PDB Molecule:probable hemolysin;
PDBTitle: c-terminal domain of probable hemolysin from chromobacterium violaceum
52d1jaka1
not modelled 71.1 5 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-N-acetylhexosaminidase catalytic domain
53d1nowa1
not modelled 70.1 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-N-acetylhexosaminidase catalytic domain
54d1qbaa3
not modelled 68.8 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-N-acetylhexosaminidase catalytic domain
55c2yl8A_
not modelled 68.3 0 PDB header:hydrolase
Chain: A: PDB Molecule:beta-n-acetylhexosaminidase;
PDBTitle: inhibition of the pneumococcal virulence factor strh and2 molecular insights into n-glycan recognition and3 hydrolysis
56d1yhta1
not modelled 68.2 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-N-acetylhexosaminidase catalytic domain
57d2z67a1
not modelled 68.1 16 Fold:PLP-dependent transferase-like
Superfamily:PLP-dependent transferases
Family:SepSecS-like
58c1nouA_
not modelled 68.0 10 PDB header:hydrolase
Chain: A: PDB Molecule:beta-hexosaminidase beta chain;
PDBTitle: native human lysosomal beta-hexosaminidase isoform b
59c1m04A_
not modelled 67.9 5 PDB header:hydrolase
Chain: A: PDB Molecule:beta-n-acetylhexosaminidase;
PDBTitle: mutant streptomyces plicatus beta-hexosaminidase (d313n) in complex2 with product (glcnac)
60c2ylaA_
not modelled 67.8 10 PDB header:hydrolase
Chain: A: PDB Molecule:beta-n-acetylhexosaminidase;
PDBTitle: inhibition of the pneumococcal virulence factor strh and2 molecular insights into n-glycan recognition and3 hydrolysis
61c3rcnA_
not modelled 67.7 5 PDB header:hydrolase
Chain: A: PDB Molecule:beta-n-acetylhexosaminidase;
PDBTitle: crystal structure of beta-n-acetylhexosaminidase from arthrobacter2 aurescens
62d2gjxa1
not modelled 67.6 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-N-acetylhexosaminidase catalytic domain
63d3deda1
not modelled 67.0 13 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
64c3gh7A_
not modelled 66.8 0 PDB header:hydrolase
Chain: A: PDB Molecule:beta-hexosaminidase;
PDBTitle: crystal structure of beta-hexosaminidase from paenibacillus2 sp. ts12 in complex with galnac
65c3nsnA_
not modelled 66.0 10 PDB header:hydrolase
Chain: A: PDB Molecule:n-acetylglucosaminidase;
PDBTitle: crystal structure of insect beta-n-acetyl-d-hexosaminidase ofhex12 complexed with tmg-chitotriomycin
66c2gjxE_
not modelled 65.3 10 PDB header:hydrolase
Chain: E: PDB Molecule:beta-hexosaminidase alpha chain;
PDBTitle: crystallographic structure of human beta-hexosaminidase a
67c3lmyA_
not modelled 64.7 10 PDB header:hydrolase
Chain: A: PDB Molecule:beta-hexosaminidase subunit beta;
PDBTitle: the crystal structure of beta-hexosaminidase b in complex with2 pyrimethamine
68c3rpmA_
not modelled 64.4 0 PDB header:hydrolase
Chain: A: PDB Molecule:beta-n-acetyl-hexosaminidase;
PDBTitle: crystal structure of the first gh20 domain of a novel beta-n-acetyl-2 hexosaminidase strh from streptococcus pneumoniae r6
69d2nqwa1
not modelled 64.2 15 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
70c1qbaA_
not modelled 62.3 10 PDB header:glycosyl hydrolase
Chain: A: PDB Molecule:chitobiase;
PDBTitle: bacterial chitobiase, glycosyl hydrolase family 20
71c2epoB_
not modelled 55.8 14 PDB header:hydrolase
Chain: B: PDB Molecule:n-acetyl-beta-d-glucosaminidase;
PDBTitle: n-acetyl-b-d-glucosaminidase (gcna) from streptococcus gordonii
72c2x24B_
not modelled 47.8 22 PDB header:ligase
Chain: B: PDB Molecule:acetyl-coa carboxylase;
PDBTitle: bovine acc2 ct domain in complex with inhibitor
73d2o1ra1
not modelled 46.0 16 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
74d2plsa1
not modelled 45.6 17 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
75d1wo8a1
not modelled 43.7 24 Fold:Methylglyoxal synthase-like
Superfamily:Methylglyoxal synthase-like
Family:Methylglyoxal synthase, MgsA
76c3ff6D_
not modelled 42.3 22 PDB header:ligase
Chain: D: PDB Molecule:acetyl-coa carboxylase 2;
PDBTitle: human acc2 ct domain with cp-640186
77c2yv1A_
not modelled 42.2 15 PDB header:ligase
Chain: A: PDB Molecule:succinyl-coa ligase [adp-forming] subunit alpha;
PDBTitle: crystal structure of succinyl-coa synthetase alpha chain from2 methanocaldococcus jannaschii dsm 2661
78c2yswB_
not modelled 42.0 13 PDB header:lyase
Chain: B: PDB Molecule:3-dehydroquinate dehydratase;
PDBTitle: crystal structure of the 3-dehydroquinate dehydratase from aquifex2 aeolicus vf5
79d1pixa3
not modelled 41.6 17 Fold:ClpP/crotonase
Superfamily:ClpP/crotonase
Family:Biotin dependent carboxylase carboxyltransferase domain
80d2bi7a1
not modelled 39.9 11 Fold:Nucleotide-binding domain
Superfamily:Nucleotide-binding domain
Family:UDP-galactopyranose mutase, N-terminal domain
81d1b93a_
not modelled 37.7 6 Fold:Methylglyoxal synthase-like
Superfamily:Methylglyoxal synthase-like
Family:Methylglyoxal synthase, MgsA
82d1vmda_
not modelled 37.1 0 Fold:Methylglyoxal synthase-like
Superfamily:Methylglyoxal synthase-like
Family:Methylglyoxal synthase, MgsA
83d1umdb1
not modelled 33.9 19 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
84d2p5ia1
not modelled 33.8 17 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:LplA-like
85d1ik6a1
not modelled 33.7 26 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
86c2uvaI_
not modelled 33.3 17 PDB header:transferase
Chain: I: PDB Molecule:fatty acid synthase beta subunits;
PDBTitle: crystal structure of fatty acid synthase from thermomyces2 lanuginosus at 3.1 angstrom resolution. this file contains3 the beta subunits of the fatty acid synthase. the entire4 crystal structure consists of one heterododecameric fatty5 acid synthase and is described in remark 400
87c1oi7A_
not modelled 32.9 16 PDB header:synthetase
Chain: A: PDB Molecule:succinyl-coa synthetase alpha chain;
PDBTitle: the crystal structure of succinyl-coa synthetase alpha2 subunit from thermus thermophilus
88d2ozlb1
not modelled 32.8 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
89d1js3a_
not modelled 32.6 14 Fold:PLP-dependent transferase-like
Superfamily:PLP-dependent transferases
Family:Pyridoxal-dependent decarboxylase
90d2r2za1
not modelled 31.7 7 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
91c3s01A_
not modelled 30.4 3 PDB header:rna binding protein
Chain: A: PDB Molecule:heterogeneous nuclear ribonucleoprotein l;
PDBTitle: crystal structure of a heterogeneous nuclear ribonucleoprotein l2 (hnrpl) from mus musculus at 2.15 a resolution
92c2yv2A_
not modelled 30.3 21 PDB header:ligase
Chain: A: PDB Molecule:succinyl-coa synthetase alpha chain;
PDBTitle: crystal structure of succinyl-coa synthetase alpha chain from2 aeropyrum pernix k1
93c3mwdB_
not modelled 29.6 10 PDB header:transferase
Chain: B: PDB Molecule:atp-citrate synthase;
PDBTitle: truncated human atp-citrate lyase with citrate bound
94c3e0dA_
not modelled 29.5 4 PDB header:transferase/dna
Chain: A: PDB Molecule:dna polymerase iii subunit alpha;
PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit
95c1od4C_
not modelled 29.4 17 PDB header:ligase
Chain: C: PDB Molecule:acetyl-coenzyme a carboxylase;
PDBTitle: acetyl-coa carboxylase carboxyltransferase domain
96c2jlhA_
not modelled 29.2 19 PDB header:protein transport
Chain: A: PDB Molecule:yop proteins translocation protein u;
PDBTitle: crystal structure of the cytoplasmic domain of yersinia2 pestis yscu n263a mutant
97c3if2B_
not modelled 28.0 10 PDB header:transferase
Chain: B: PDB Molecule:aminotransferase;
PDBTitle: crystal structure of putative amino-acid aminotransferase2 (yp_265399.1) from psychrobacter arcticum 273-4 at 2.50 a resolution
98c2dgxA_
not modelled 26.7 3 PDB header:rna binding protein
Chain: A: PDB Molecule:kiaa0430 protein;
PDBTitle: solution structure of the rna recognition motif in kiaa04302 protein
99d2r8oa1
not modelled 26.4 14 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
100d1jmta_
not modelled 25.6 11 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Splicing factor U2AF subunits
101c2hnhA_
not modelled 25.6 4 PDB header:transferase
Chain: A: PDB Molecule:dna polymerase iii alpha subunit;
PDBTitle: crystal structure of the catalytic alpha subunit of e. coli2 replicative dna polymerase iii
102d1zoda1
not modelled 25.6 4 Fold:PLP-dependent transferase-like
Superfamily:PLP-dependent transferases
Family:GABA-aminotransferase-like
103c2dnoA_
not modelled 25.5 3 PDB header:rna binding protein
Chain: A: PDB Molecule:trinucleotide repeat containing 4 variant;
PDBTitle: solution structure of rna binding domain in trinucleotide2 repeat containing 4 variant
104c3ez4B_
not modelled 25.2 10 PDB header:transferase
Chain: B: PDB Molecule:3-methyl-2-oxobutanoate hydroxymethyltransferase;
PDBTitle: crystal structure of 3-methyl-2-oxobutanoate2 hydroxymethyltransferase from burkholderia pseudomallei
105d1itza2
not modelled 25.1 12 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
106d1qs0b1
not modelled 24.6 19 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
107c1pixB_
not modelled 24.4 17 PDB header:lyase
Chain: B: PDB Molecule:glutaconyl-coa decarboxylase a subunit;
PDBTitle: crystal structure of the carboxyltransferase subunit of the2 bacterial ion pump glutaconyl-coenzyme a decarboxylase
108c3llbA_
not modelled 24.0 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: the crystal structure of the protein pa3983 with unknown2 function from pseudomonas aeruginosa pao1
109d1w85b1
not modelled 23.3 15 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
110d2rk5a1
not modelled 23.0 11 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
111d1c7ga_
not modelled 23.0 22 Fold:PLP-dependent transferase-like
Superfamily:PLP-dependent transferases
Family:Beta-eliminating lyases
112c3glmD_
not modelled 22.2 8 PDB header:lyase
Chain: D: PDB Molecule:glutaconyl-coa decarboxylase subunit a;
PDBTitle: glutaconyl-coa decarboxylase a subunit from clostridium2 symbiosum co-crystallized with crotonyl-coa
113c3bzrA_
not modelled 22.1 15 PDB header:membrane protein, protein transport
Chain: A: PDB Molecule:escu;
PDBTitle: crystal structure of escu c-terminal domain with n262d mutation, space2 group p 41 21 2
114d3bzra1
not modelled 22.1 15 Fold:EscU C-terminal domain-like
Superfamily:EscU C-terminal domain-like
Family:EscU C-terminal domain-like
115d1knxa1
not modelled 21.6 21 Fold:MurF and HprK N-domain-like
Superfamily:HprK N-terminal domain-like
Family:HPr kinase/phoshatase HprK N-terminal domain
116c3e02A_
not modelled 21.6 4 PDB header:metal binding protein
Chain: A: PDB Molecule:uncharacterized protein duf849;
PDBTitle: crystal structure of a duf849 family protein (bxe_c0271) from2 burkholderia xenovorans lb400 at 1.90 a resolution
117c3h0jA_
not modelled 21.3 17 PDB header:transferase
Chain: A: PDB Molecule:acetyl-coa carboxylase;
PDBTitle: crystal structure of the carboxyltransferase domain of2 acetyl-coenzyme a carboxylase in complex with compound 2
118c1uytC_
not modelled 21.2 17 PDB header:transferase
Chain: C: PDB Molecule:acetyl-coa carboxylase;
PDBTitle: acetyl-coa carboxylase carboxyltransferase domain
119d1sffa_
not modelled 20.9 13 Fold:PLP-dependent transferase-like
Superfamily:PLP-dependent transferases
Family:GABA-aminotransferase-like
120d2o3ga1
not modelled 20.8 19 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like

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