Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP21170
DateThu Jan 5 11:37:56 GMT 2012
Unique Job ID79aafb9f0541a419

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3nzqB_
Top template information
PDB header:lyase
Chain: B: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600
Confidence and coverage
Confidence:100.0% Coverage: 95%
625 residues ( 95% 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  MSDDMSMGLPSSAGEHGVLRSMQEVAMSSQEASKMLRTYNIAWWGNNYYDVNELGHISVC
Secondary structure 
SS confidence 
Disorder  ???????
?
???
???
?????????
?
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  PDPDVPEARVDLAQLVKTREAQGQRLPALFCFPQILQHRLRSINAAFKRARESYGYNGDY
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  FLVYPIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYI
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  RLALIGEKMGHKVYLVIEKMSEIAIVLDEAERLNVVPRLGVRARLASQGSGKWQSSGGEK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  SKFGLAATQVLQLVETLREAGRLDSLQLLHFHLGSQMANIRDIATGVRESARFYVELHKL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  GVNIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGDACEENGLPHPTVITE
Secondary structure 
SS confidence 
Disorder 
?
???????
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  SGRAVTAHHTVLVSNIIGVERNEYTVPTAPAEDAPRALQSMWETWQEMHEPGTRRSLREW
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  LHDSQMDLHDIHIGYSSGIFSLQERAWAEQLYLSMCHEVQKQLDPQNRAHRPIIDELQER
Secondary structure 
SS confidence 
Disorder 
?
?????????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  MADKMYVNFSLFQSMPDAWGIDQLFPVLPLEGLDQVPERRAVLLDITCDSDGAIDHYIDG
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  DGIATTMPMPEYDPENPPMLGFFMVGAYQEILGNMHNLFGDTEAVDVFVFPDGSVEVELS
Secondary structure 
SS confidence 
Disorder  ?????
Disorder confidence 
 
   .........610.........620.........630.........640.........650........
Sequence  DEGDTVADMLQYVQLDPKTLLTQFRDQVKKTDLDAELQQQFLEEFEAGLYGYTYLEDE
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 3nzq chain B

3D model

Region: 34 - 658
Aligned: 625
Modelled: 625
Confidence: 100.0%
Identity: 100%
PDB header:lyase
Chain: B: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600

Phyre2

PDB 3n2o chain A

3D model

Region: 31 - 657
Aligned: 625
Modelled: 627
Confidence: 100.0%
Identity: 55%
PDB header:lyase
Chain: A: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: x-ray crystal structure of arginine decarboxylase complexed with2 arginine from vibrio vulnificus

Phyre2

PDB 3nzp chain A

3D model

Region: 39 - 656
Aligned: 571
Modelled: 590
Confidence: 100.0%
Identity: 35%
PDB header:lyase
Chain: A: PDB Molecule:arginine decarboxylase;
PDBTitle: crystal structure of the biosynthetic arginine decarboxylase spea from2 campylobacter jejuni, northeast structural genomics consortium target3 br53

Phyre2

PDB 2o0t chain B

3D model

Region: 44 - 611
Aligned: 422
Modelled: 458
Confidence: 100.0%
Identity: 24%
PDB header:lyase
Chain: B: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: the three dimensional structure of diaminopimelate decarboxylase from2 mycobacterium tuberculosis reveals a tetrameric enzyme organisation

Phyre2

PDB 1tuf chain A

3D model

Region: 45 - 611
Aligned: 419
Modelled: 444
Confidence: 100.0%
Identity: 22%
PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of diaminopimelate decarboxylase from m.2 jannaschi

Phyre2

PDB 1knw chain A

3D model

Region: 71 - 611
Aligned: 391
Modelled: 424
Confidence: 100.0%
Identity: 19%
PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of diaminopimelate decarboxylase

Phyre2

PDB 1d7k chain B

3D model

Region: 72 - 588
Aligned: 376
Modelled: 426
Confidence: 100.0%
Identity: 20%
PDB header:lyase
Chain: B: PDB Molecule:human ornithine decarboxylase;
PDBTitle: crystal structure of human ornithine decarboxylase at 2.12 angstroms resolution

Phyre2

PDB 2on3 chain A

3D model

Region: 67 - 588
Aligned: 367
Modelled: 402
Confidence: 100.0%
Identity: 20%
PDB header:lyase
Chain: A: PDB Molecule:ornithine decarboxylase;
PDBTitle: a structural insight into the inhibition of human and2 leishmania donovani ornithine decarboxylases by 3-aminooxy-3 1-aminopropane

Phyre2

PDB 3n2b chain D

3D model

Region: 48 - 611
Aligned: 388
Modelled: 410
Confidence: 100.0%
Identity: 23%
PDB header:lyase
Chain: D: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: 1.8 angstrom resolution crystal structure of diaminopimelate2 decarboxylase (lysa) from vibrio cholerae.

Phyre2

PDB 2qgh chain A

3D model

Region: 71 - 611
Aligned: 387
Modelled: 426
Confidence: 100.0%
Identity: 21%
PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of diaminopimelate decarboxylase from helicobacter2 pylori complexed with l-lysine

Phyre2

PDB 3btn chain A

3D model

Region: 67 - 588
Aligned: 355
Modelled: 419
Confidence: 100.0%
Identity: 19%
PDB header:biosynthetic protein
Chain: A: PDB Molecule:antizyme inhibitor 1;
PDBTitle: crystal structure of antizyme inhibitor, an ornithine2 decarboxylase homologous protein

Phyre2

PDB 2p3e chain A

3D model

Region: 46 - 611
Aligned: 387
Modelled: 420
Confidence: 100.0%
Identity: 22%
PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of aq1208 from aquifex aeolicus

Phyre2

PDB 2plj chain A

3D model

Region: 72 - 588
Aligned: 353
Modelled: 394
Confidence: 100.0%
Identity: 25%
PDB header:lyase
Chain: A: PDB Molecule:lysine/ornithine decarboxylase;
PDBTitle: crystal structure of lysine/ornithine decarboxylase complexed with2 putrescine from vibrio vulnificus

Phyre2

PDB 2j66 chain A

3D model

Region: 69 - 611
Aligned: 384
Modelled: 432
Confidence: 100.0%
Identity: 19%
PDB header:lyase
Chain: A: PDB Molecule:btrk;
PDBTitle: structural characterisation of btrk decarboxylase from2 butirosin biosynthesis

Phyre2

PDB 2yxx chain A

3D model

Region: 74 - 611
Aligned: 380
Modelled: 421
Confidence: 100.0%
Identity: 22%
PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure analysis of diaminopimelate decarboxylate (lysa)

Phyre2

PDB 2nva chain H

3D model

Region: 72 - 587
Aligned: 363
Modelled: 419
Confidence: 100.0%
Identity: 24%
PDB header:lyase
Chain: H: PDB Molecule:arginine decarboxylase, a207r protein;
PDBTitle: the x-ray crystal structure of the paramecium bursaria2 chlorella virus arginine decarboxylase bound to agmatine

Phyre2

PDB 1twi chain A domain 2

3D model

Region: 93 - 369
Aligned: 260
Modelled: 277
Confidence: 100.0%
Identity: 23%
Fold: TIM beta/alpha-barrel
Superfamily: PLP-binding barrel
Family: Alanine racemase-like, N-terminal domain

Phyre2

PDB 3mt1 chain B

3D model

Region: 83 - 614
Aligned: 348
Modelled: 398
Confidence: 100.0%
Identity: 18%
PDB header:lyase
Chain: B: PDB Molecule:putative carboxynorspermidine decarboxylase protein;
PDBTitle: crystal structure of putative carboxynorspermidine decarboxylase2 protein from sinorhizobium meliloti

Phyre2

PDB 3n29 chain A

3D model

Region: 82 - 597
Aligned: 346
Modelled: 400
Confidence: 100.0%
Identity: 17%
PDB header:lyase
Chain: A: PDB Molecule:carboxynorspermidine decarboxylase;
PDBTitle: crystal structure of carboxynorspermidine decarboxylase complexed with2 norspermidine from campylobacter jejuni

Phyre2

PDB 1knw chain A domain 2

3D model

Region: 92 - 370
Aligned: 242
Modelled: 266
Confidence: 100.0%
Identity: 18%
Fold: TIM beta/alpha-barrel
Superfamily: PLP-binding barrel
Family: Alanine racemase-like, N-terminal domain

Phyre2

PDB 2k2e chain A

3D model

Region: 25 - 63
Aligned: 36
Modelled: 36
Confidence: 68.0%
Identity: 19%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein bp2786;
PDBTitle: solution nmr structure of bordetella pertussis protein2 bp2786, a mth938-like domain. northeast structural3 genomics consortium target ber31

Phyre2

PDB 2dex chain X domain 3

3D model

Region: 1 - 91
Aligned: 87
Modelled: 87
Confidence: 58.3%
Identity: 18%
Fold: Pentein, beta/alpha-propeller
Superfamily: Pentein
Family: Peptidylarginine deiminase Pad4, catalytic C-terminal domain

Phyre2
1
c3nzqB_
2
c3n2oA_
3
c3nzpA_
4
c2o0tB_
5
c1tufA_
6
c1knwA_
7
c1d7kB_
8
c2on3A_
9
c3n2bD_
10
c2qghA_
11
c3btnA_
12
c2p3eA_
13
c2pljA_
14
c2j66A_
15
c2yxxA_
16
c2nvaH_
17
d1twia2
18
c3mt1B_
19
c3n29A_
20
d1knwa2
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
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40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
c2k2eA_
61
62
63
64
65
d2dexx3
66
67
68
69
70
71
72
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75
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3nzqB_
100.0 100 PDB header:lyase
Chain: B: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600
2c3n2oA_
100.0 55 PDB header:lyase
Chain: A: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: x-ray crystal structure of arginine decarboxylase complexed with2 arginine from vibrio vulnificus
3c3nzpA_
100.0 35 PDB header:lyase
Chain: A: PDB Molecule:arginine decarboxylase;
PDBTitle: crystal structure of the biosynthetic arginine decarboxylase spea from2 campylobacter jejuni, northeast structural genomics consortium target3 br53
4c2o0tB_
100.0 24 PDB header:lyase
Chain: B: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: the three dimensional structure of diaminopimelate decarboxylase from2 mycobacterium tuberculosis reveals a tetrameric enzyme organisation
5c1tufA_
100.0 22 PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of diaminopimelate decarboxylase from m.2 jannaschi
6c1knwA_
100.0 19 PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of diaminopimelate decarboxylase
7c1d7kB_
100.0 20 PDB header:lyase
Chain: B: PDB Molecule:human ornithine decarboxylase;
PDBTitle: crystal structure of human ornithine decarboxylase at 2.12 angstroms resolution
8c2on3A_
100.0 20 PDB header:lyase
Chain: A: PDB Molecule:ornithine decarboxylase;
PDBTitle: a structural insight into the inhibition of human and2 leishmania donovani ornithine decarboxylases by 3-aminooxy-3 1-aminopropane
9c3n2bD_
100.0 23 PDB header:lyase
Chain: D: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: 1.8 angstrom resolution crystal structure of diaminopimelate2 decarboxylase (lysa) from vibrio cholerae.
10c2qghA_
100.0 21 PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of diaminopimelate decarboxylase from helicobacter2 pylori complexed with l-lysine
11c3btnA_
100.0 19 PDB header:biosynthetic protein
Chain: A: PDB Molecule:antizyme inhibitor 1;
PDBTitle: crystal structure of antizyme inhibitor, an ornithine2 decarboxylase homologous protein
12c2p3eA_
100.0 22 PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure of aq1208 from aquifex aeolicus
13c2pljA_
100.0 25 PDB header:lyase
Chain: A: PDB Molecule:lysine/ornithine decarboxylase;
PDBTitle: crystal structure of lysine/ornithine decarboxylase complexed with2 putrescine from vibrio vulnificus
14c2j66A_
100.0 19 PDB header:lyase
Chain: A: PDB Molecule:btrk;
PDBTitle: structural characterisation of btrk decarboxylase from2 butirosin biosynthesis
15c2yxxA_
100.0 22 PDB header:lyase
Chain: A: PDB Molecule:diaminopimelate decarboxylase;
PDBTitle: crystal structure analysis of diaminopimelate decarboxylate (lysa)
16c2nvaH_
100.0 24 PDB header:lyase
Chain: H: PDB Molecule:arginine decarboxylase, a207r protein;
PDBTitle: the x-ray crystal structure of the paramecium bursaria2 chlorella virus arginine decarboxylase bound to agmatine
17d1twia2
100.0 23 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
18c3mt1B_
100.0 18 PDB header:lyase
Chain: B: PDB Molecule:putative carboxynorspermidine decarboxylase protein;
PDBTitle: crystal structure of putative carboxynorspermidine decarboxylase2 protein from sinorhizobium meliloti
19c3n29A_
100.0 17 PDB header:lyase
Chain: A: PDB Molecule:carboxynorspermidine decarboxylase;
PDBTitle: crystal structure of carboxynorspermidine decarboxylase complexed with2 norspermidine from campylobacter jejuni
20d1knwa2
100.0 18 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
21d1hkva2
not modelled 100.0 23 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
22c1njjC_
not modelled 100.0 21 PDB header:lyase
Chain: C: PDB Molecule:ornithine decarboxylase;
PDBTitle: crystal structure determination of t. brucei ornithine2 decarboxylase bound to d-ornithine and to g418
23d1d7ka2
not modelled 100.0 19 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
24d1f3ta2
not modelled 100.0 22 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
25d7odca2
not modelled 100.0 22 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
26c3anuA_
not modelled 99.9 11 PDB header:lyase
Chain: A: PDB Molecule:d-serine dehydratase;
PDBTitle: crystal structure of d-serine dehydratase from chicken kidney
27c3gwqB_
not modelled 99.9 14 PDB header:lyase
Chain: B: PDB Molecule:d-serine deaminase;
PDBTitle: crystal structure of a putative d-serine deaminase (bxe_a4060) from2 burkholderia xenovorans lb400 at 2.00 a resolution
28c3llxA_
not modelled 99.8 13 PDB header:isomerase
Chain: A: PDB Molecule:predicted amino acid aldolase or racemase;
PDBTitle: crystal structure of an ala racemase-like protein (il1761) from2 idiomarina loihiensis at 1.50 a resolution
29c1xfcB_
not modelled 99.8 17 PDB header:isomerase
Chain: B: PDB Molecule:alanine racemase;
PDBTitle: the 1.9 a crystal structure of alanine racemase from mycobacterium2 tuberculosis contains a conserved entryway into the active site
30c3kw3B_
not modelled 99.7 10 PDB header:isomerase
Chain: B: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of alanine racemase from bartonella henselae with2 covalently bound pyridoxal phosphate
31c3oo2B_
not modelled 99.6 11 PDB header:isomerase
Chain: B: PDB Molecule:alanine racemase 1;
PDBTitle: 2.37 angstrom resolution crystal structure of an alanine racemase2 (alr) from staphylococcus aureus subsp. aureus col
32c2dy3B_
not modelled 99.6 15 PDB header:isomerase
Chain: B: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of alanine racemase from corynebacterium glutamicum
33c1w8gA_
not modelled 99.5 14 PDB header:plp-binding protein
Chain: A: PDB Molecule:hypothetical upf0001 protein yggs;
PDBTitle: crystal structure of e. coli k-12 yggs
34c1vftA_
not modelled 99.4 16 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of l-cycloserine-bound form of alanine2 racemase from d-cycloserine-producing streptomyces3 lavendulae
35d1hkva1
not modelled 99.4 27 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
36d1vfsa2
not modelled 99.4 19 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
37c3oo2A_
not modelled 99.4 10 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase 1;
PDBTitle: 2.37 angstrom resolution crystal structure of an alanine racemase2 (alr) from staphylococcus aureus subsp. aureus col
38c3r79B_
not modelled 99.3 15 PDB header:structure genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of an uncharactertized protein from agrobacterium2 tumefaciens
39c3e6eC_
not modelled 99.3 12 PDB header:isomerase
Chain: C: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of alanine racemase from e.faecalis2 complex with cycloserine
40d1rcqa2
not modelled 99.2 15 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
41c3hurA_
not modelled 99.2 13 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of alanine racemase from oenococcus oeni
42c2odoC_
not modelled 99.2 14 PDB header:isomerase
Chain: C: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of pseudomonas fluorescens alanine racemase
43c3cpgA_
not modelled 99.2 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of an unknown protein from bifidobacterium2 adolescentis
44d1bd0a2
not modelled 99.2 11 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:Alanine racemase-like, N-terminal domain
45d1knwa1
not modelled 99.2 22 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
46d1twia1
not modelled 99.1 22 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
47c3mubB_
not modelled 99.0 16 PDB header:isomerase
Chain: B: PDB Molecule:alanine racemase;
PDBTitle: the crystal structure of alanine racemase from streptococcus2 pneumoniae
48d7odca1
not modelled 99.0 23 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
49c1niuA_
not modelled 98.9 12 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase;
PDBTitle: alanine racemase with bound inhibitor derived from l-2 cycloserine
50c2rjgC_
not modelled 98.9 12 PDB header:isomerase
Chain: C: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of biosynthetic alaine racemase from escherichia2 coli
51c3co8B_
not modelled 98.8 14 PDB header:isomerase
Chain: B: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of alanine racemase from oenococcus oeni
52d1d7ka1
not modelled 98.7 23 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
53d1f3ta1
not modelled 98.7 22 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
54d1ct5a_
not modelled 97.8 13 Fold:TIM beta/alpha-barrel
Superfamily:PLP-binding barrel
Family:"Hypothetical" protein ybl036c
55d1njjb1
not modelled 97.7 26 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
56c2vd9A_
not modelled 96.9 14 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase;
PDBTitle: the crystal structure of alanine racemase from bacillus2 anthracis (ba0252) with bound l-ala-p
57d2toda1
not modelled 96.8 24 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily:Alanine racemase C-terminal domain-like
Family:Eukaryotic ODC-like
58c2zq0B_
not modelled 74.1 13 PDB header:hydrolase
Chain: B: PDB Molecule:alpha-glucosidase (alpha-glucosidase susb);
PDBTitle: crystal structure of susb complexed with acarbose
59d1z41a1
not modelled 70.2 15 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
60c2k2eA_
68.0 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein bp2786;
PDBTitle: solution nmr structure of bordetella pertussis protein2 bp2786, a mth938-like domain. northeast structural3 genomics consortium target ber31
61c1us2A_
not modelled 67.9 19 PDB header:hydrolase
Chain: A: PDB Molecule:endo-beta-1,4-xylanase;
PDBTitle: xylanase10c (mutant e385a) from cellvibrio japonicus in2 complex with xylopentaose
62c1iszA_
not modelled 64.6 20 PDB header:hydrolase
Chain: A: PDB Molecule:endo-1,4-beta-d-xylanase;
PDBTitle: crystal structure of xylanase from streptomyces2 olivaceoviridis e-86 complexed with galactose
63c2gm2A_
not modelled 64.6 31 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: nmr structure of xanthomonas campestris xcc1710: northeast2 structural genomics consortium target xcr35
64c2h1xB_
not modelled 60.0 21 PDB header:hydrolase
Chain: B: PDB Molecule:5-hydroxyisourate hydrolase (formerly known as
PDBTitle: crystal structure of 5-hydroxyisourate hydrolase (formerly2 known as trp, transthyretin related protein)
65d2dexx3
58.3 18 Fold:Pentein, beta/alpha-propeller
Superfamily:Pentein
Family:Peptidylarginine deiminase Pad4, catalytic C-terminal domain
66d1l1ea_
not modelled 57.4 11 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Mycolic acid cyclopropane synthase
67d1r85a_
not modelled 53.7 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
68d1tf3a3
not modelled 51.9 55 Fold:beta-beta-alpha zinc fingers
Superfamily:beta-beta-alpha zinc fingers
Family:Classic zinc finger, C2H2
69c3hrdE_
not modelled 51.4 28 PDB header:oxidoreductase
Chain: E: PDB Molecule:nicotinate dehydrogenase large molybdopterin
PDBTitle: crystal structure of nicotinate dehydrogenase
70d2fk8a1
not modelled 50.7 11 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Mycolic acid cyclopropane synthase
71d2ha9a1
not modelled 49.1 14 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:SP0239-like
72c2g5xA_
not modelled 48.3 18 PDB header:hydrolase
Chain: A: PDB Molecule:ribosome-inactivating protein;
PDBTitle: crystal structure of lychnin a type 1 ribosome inactivating2 protein (rip)
73c2w54F_
not modelled 46.7 27 PDB header:oxidoreductase
Chain: F: PDB Molecule:xanthine dehydrogenase;
PDBTitle: crystal structure of xanthine dehydrogenase from2 rhodobacter capsulatus in complex with bound inhibitor3 pterin-6-aldehyde
74c3kruC_
not modelled 45.9 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:nadh:flavin oxidoreductase/nadh oxidase;
PDBTitle: crystal structure of the thermostable old yellow enzyme from2 thermoanaerobacter pseudethanolicus e39
75d1ps9a1
not modelled 45.2 14 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
76c3eubL_
not modelled 44.1 20 PDB header:oxidoreductase
Chain: L: PDB Molecule:xanthine dehydrogenase/oxidase;
PDBTitle: crystal structure of desulfo-xanthine oxidase with xanthine
77c3gr7A_
not modelled 43.5 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadph dehydrogenase;
PDBTitle: structure of oye from geobacillus kaustophilus, hexagonal2 crystal form
78c3hf3A_
not modelled 42.8 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:chromate reductase;
PDBTitle: old yellow enzyme from thermus scotoductus sa-01
79c1ps9A_
not modelled 41.5 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:2,4-dienoyl-coa reductase;
PDBTitle: the crystal structure and reaction mechanism of e. coli 2,4-2 dienoyl coa reductase
80d1v97a5
not modelled 40.2 20 Fold:Molybdenum cofactor-binding domain
Superfamily:Molybdenum cofactor-binding domain
Family:Molybdenum cofactor-binding domain
81c1wygA_
not modelled 39.8 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:xanthine dehydrogenase/oxidase;
PDBTitle: crystal structure of a rat xanthine dehydrogenase triple mutant2 (c535a, c992r and c1324s)
82d1jsca3
not modelled 39.4 20 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
83c2b5dX_
not modelled 39.4 9 PDB header:hydrolase
Chain: X: PDB Molecule:alpha-amylase;
PDBTitle: crystal structure of the novel alpha-amylase amyc from thermotoga2 maritima
84d1jrob2
not modelled 39.1 27 Fold:Molybdenum cofactor-binding domain
Superfamily:Molybdenum cofactor-binding domain
Family:Molybdenum cofactor-binding domain
85c2zvrA_
not modelled 37.9 17 PDB header:isomerase
Chain: A: PDB Molecule:uncharacterized protein tm_0416;
PDBTitle: crystal structure of a d-tagatose 3-epimerase-related2 protein from thermotoga maritima
86d1vyra_
not modelled 37.8 14 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
87d2ji7a3
not modelled 37.5 25 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase PP module
88d1ffvb2
not modelled 36.9 29 Fold:Molybdenum cofactor-binding domain
Superfamily:Molybdenum cofactor-binding domain
Family:Molybdenum cofactor-binding domain
89d1qo7a_
not modelled 36.4 17 Fold:alpha/beta-Hydrolases
Superfamily:alpha/beta-Hydrolases
Family:Epoxide hydrolase
90c1ydoC_
not modelled 36.4 18 PDB header:lyase
Chain: C: PDB Molecule:hmg-coa lyase;
PDBTitle: crystal structure of the bacillis subtilis hmg-coa lyase, northeast2 structural genomics target sr181.
91d1rm6a2
not modelled 35.4 17 Fold:Molybdenum cofactor-binding domain
Superfamily:Molybdenum cofactor-binding domain
Family:Molybdenum cofactor-binding domain
92c2h90A_
not modelled 35.1 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:xenobiotic reductase a;
PDBTitle: xenobiotic reductase a in complex with coumarin
93d2glka1
not modelled 34.6 18 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
94d1kpga_
not modelled 34.5 13 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Mycolic acid cyclopropane synthase
95d1n62b2
not modelled 33.4 27 Fold:Molybdenum cofactor-binding domain
Superfamily:Molybdenum cofactor-binding domain
Family:Molybdenum cofactor-binding domain
96c1sb3D_
not modelled 31.9 17 PDB header:oxidoreductase
Chain: D: PDB Molecule:4-hydroxybenzoyl-coa reductase alpha subunit;
PDBTitle: structure of 4-hydroxybenzoyl-coa reductase from thauera2 aromatica
97c2gpzC_
not modelled 31.1 22 PDB header:hydrolase
Chain: C: PDB Molecule:transthyretin-like protein;
PDBTitle: transthyretin-like protein from salmonella dublin
98d1xlma_
not modelled 30.9 19 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
99d1vlba4
not modelled 30.6 15 Fold:Molybdenum cofactor-binding domain
Superfamily:Molybdenum cofactor-binding domain
Family:Molybdenum cofactor-binding domain
100c2fk8A_
not modelled 30.5 11 PDB header:transferase
Chain: A: PDB Molecule:methoxy mycolic acid synthase 4;
PDBTitle: crystal structure of hma (mmaa4) from mycobacterium tuberculosis2 complexed with s-adenosylmethionine
101d1bxca_
not modelled 30.1 17 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
102d1wxma1
not modelled 29.8 30 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ras-binding domain, RBD
103c1kblA_
not modelled 29.7 18 PDB header:transferase
Chain: A: PDB Molecule:pyruvate phosphate dikinase;
PDBTitle: pyruvate phosphate dikinase
104d2b5dx2
not modelled 29.2 9 Fold:7-stranded beta/alpha barrel
Superfamily:Glycoside hydrolase/deacetylase
Family:AmyC N-terminal domain-like
105d1qt1a_
not modelled 29.0 18 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
106d1w32a_
not modelled 28.4 17 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
107d1s4ea2
not modelled 28.4 19 Fold:Ferredoxin-like
Superfamily:GHMP Kinase, C-terminal domain
Family:Galactokinase
108c2ojlB_
not modelled 28.2 22 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of q7waf1_borpa from bordetella parapertussis.2 northeast structural genomics target bpr68.
109c3dtyA_
not modelled 27.6 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:oxidoreductase, gfo/idh/moca family;
PDBTitle: crystal structure of an oxidoreductase from pseudomonas2 syringae
110c1ffvB_
not modelled 27.5 29 PDB header:hydrolase
Chain: B: PDB Molecule:cutl, molybdoprotein of carbon monoxide
PDBTitle: carbon monoxide dehydrogenase from hydrogenophaga2 pseudoflava
111c1jscA_
not modelled 27.4 20 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
112c1t3qB_
not modelled 27.4 25 PDB header:oxidoreductase
Chain: B: PDB Molecule:quinoline 2-oxidoreductase large subunit;
PDBTitle: crystal structure of quinoline 2-oxidoreductase from pseudomonas2 putida 86
113c1n62E_
not modelled 27.3 27 PDB header:oxidoreductase
Chain: E: PDB Molecule:carbon monoxide dehydrogenase large chain;
PDBTitle: crystal structure of the mo,cu-co dehydrogenase (codh), n-2 butylisocyanide-bound state
114d2fi9a1
not modelled 26.4 24 Fold:MTH938-like
Superfamily:MTH938-like
Family:MTH938-like
115d1lqaa_
not modelled 25.7 18 Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
116c1tx2A_
not modelled 25.5 24 PDB header:transferase
Chain: A: PDB Molecule:dhps, dihydropteroate synthase;
PDBTitle: dihydropteroate synthetase, with bound inhibitor manic, from bacillus2 anthracis
117d1tx2a_
not modelled 25.5 24 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
118c2p10D_
not modelled 25.3 11 PDB header:hydrolase
Chain: D: PDB Molecule:mll9387 protein;
PDBTitle: crystal structure of a putative phosphonopyruvate hydrolase (mll9387)2 from mesorhizobium loti maff303099 at 2.15 a resolution
119c3dexA_
not modelled 24.9 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:sav_2001;
PDBTitle: crystal structure of sav_2001 protein from streptomyces2 avermitilis, northeast structural genomics consortium3 target svr107.
120d1bxba_
not modelled 24.4 18 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase

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