Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP75793
DateThu Jan 5 12:14:12 GMT 2012
Unique Job IDd2fbd53b3753589c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1r9da_
Top template information
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
Confidence and coverage
Confidence:100.0% Coverage: 97%
782 residues ( 97% 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  MTTLKLDTLSDRIKAHKNALVHIVKPPVCTERAQHYTEMYQQHLDKPIPVRRALALAHHL
Secondary structure 
SS confidence 
Disorder  ????????
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ANRTIWIKHDELIIGNQASEVRAAPIFPEYTVSWIEKEIDDLADRPGAGFAVSEENKRVL
Secondary structure 
SS confidence 
Disorder 
?
??
?????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  HEVCPWWRGQTVQDRCYGMFTDEQKGLLATGIIKAEGNMTSGDAHLAVNFPLLLEKGLDG
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LREEVAERRSRINLTVLEDLHGEQFLKAIDIVLVAVSEHIERFAALAREMAATETRESRR
Secondary structure 
SS confidence 
Disorder 
????????
?????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  DELLAMAENCDLIAHQPPQTFWQALQLCYFIQLILQIESNGHSVSFGRMDQYLYPYYRRD
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  VELNQTLDREHAIEMLHSCWLKLLEVNKIRSGSHSKASAGSPLYQNVTIGGQNLVDGQPM
Secondary structure 
SS confidence 
Disorder 
????
????
?
?
??
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  DAVNPLSYAILESCGRLRSTQPNLSVRYHAGMSNDFLDACVQVIRCGFGMPAFNNDEIVI
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  PEFIKLGIEPQDAYDYAAIGCIETAVGGKWGYRCTGMSFINFARVMLAALEGGHDATSGK
Secondary structure 
SS confidence 
Disorder 
?
?????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  VFLPQEKALSAGNFNNFDEVMDAWDTQIRYYTRKSIEIEYVVDTMLEENVHDILCSALVD
Secondary structure 
SS confidence 
Disorder 
?????
????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  DCIERAKSIKQGGAKYDWVSGLQVGIANLGNSLAAVKKLVFEQGAIGQQQLAAALADDFD
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  GLTHEQLRQRLINGAPKYGNDDDTVDTLLARAYQTYIDELKQYHNPRYGRGPVGGNYYAG
Secondary structure 
SS confidence 
Disorder 
?
?
????
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  TSSISANVPFGAQTMATPDGRKAHTPLAEGASPASGTDHLGPTAVIGSVGKLPTAAILGG
Secondary structure 
SS confidence 
Disorder 
????????
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  VLLNQKLNPATLENESDKQKLMILLRTFFEVHKGWHIQYNIVSRETLLDAKKHPDQYRDL
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........790.........800.........810
Sequence  VVRVAGYSAFFTALSPDAQDDIIARTEHML
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 1r9d chain A

3D model

Region: 6 - 810
Aligned: 782
Modelled: 797
Confidence: 100.0%
Identity: 38%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 2y8n chain C

3D model

Region: 10 - 809
Aligned: 780
Modelled: 800
Confidence: 100.0%
Identity: 28%
PDB header:lyase
Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit;
PDBTitle: crystal structure of glycyl radical enzyme

Phyre2

PDB 2f3o chain B

3D model

Region: 11 - 810
Aligned: 772
Modelled: 794
Confidence: 100.0%
Identity: 32%
PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus

Phyre2

PDB 1h16 chain A

3D model

Region: 59 - 809
Aligned: 667
Modelled: 727
Confidence: 100.0%
Identity: 26%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1qhm chain A

3D model

Region: 59 - 672
Aligned: 531
Modelled: 599
Confidence: 100.0%
Identity: 22%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1hk8 chain A

3D model

Region: 116 - 746
Aligned: 441
Modelled: 488
Confidence: 99.4%
Identity: 18%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: Class III anaerobic ribonucleotide reductase NRDD subunit

Phyre2

PDB 1hk8 chain A

3D model

Region: 116 - 746
Aligned: 441
Modelled: 492
Confidence: 99.4%
Identity: 18%
PDB header:oxidoreductase
Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase;
PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp

Phyre2

PDB 1qkr chain A

3D model

Region: 207 - 248
Aligned: 42
Modelled: 42
Confidence: 71.1%
Identity: 24%
Fold: Four-helical up-and-down bundle
Superfamily: alpha-catenin/vinculin-like
Family: alpha-catenin/vinculin

Phyre2

PDB 1r0k chain A domain 1

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 63.9%
Identity: 28%
Fold: Left-handed superhelix
Superfamily: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Family: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

Phyre2

PDB 3gr1 chain A

3D model

Region: 718 - 761
Aligned: 40
Modelled: 44
Confidence: 63.2%
Identity: 18%
PDB header:membrane protein
Chain: A: PDB Molecule:protein prgh;
PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392)

Phyre2

PDB 1q0q chain A domain 1

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 48.6%
Identity: 21%
Fold: Left-handed superhelix
Superfamily: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Family: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain

Phyre2

PDB 2jcy chain A

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 45.1%
Identity: 21%
PDB header:oxidoreductase
Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis

Phyre2

PDB 3au9 chain A

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 44.5%
Identity: 23%
PDB header:isomerase/isomerase inhibitor
Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: crystal structure of the quaternary complex-1 of an isomerase

Phyre2

PDB 1r0l chain D

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 44.1%
Identity: 28%
PDB header:oxidoreductase
Chain: D: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: 1-deoxy-d-xylulose 5-phosphate reductoisomerase from2 zymomonas mobilis in complex with nadph

Phyre2

PDB 1v9x chain A

3D model

Region: 60 - 125
Aligned: 66
Modelled: 66
Confidence: 42.2%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:poly (adp-ribose) polymerase;
PDBTitle: solution structure of the first zn-finger domain of2 poly(adp-ribose) polymerase-1

Phyre2

PDB 3ode chain A

3D model

Region: 60 - 125
Aligned: 66
Modelled: 66
Confidence: 38.5%
Identity: 18%
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1;
PDBTitle: human parp-1 zinc finger 2 (zn2) bound to dna

Phyre2

PDB 3gr0 chain D

3D model

Region: 718 - 761
Aligned: 40
Modelled: 44
Confidence: 32.4%
Identity: 18%
PDB header:membrane protein
Chain: D: PDB Molecule:protein prgh;
PDBTitle: periplasmic domain of the t3ss inner membrane protein prgh from2 s.typhimurium (fragment 170-362)

Phyre2

PDB 2cs2 chain A

3D model

Region: 60 - 125
Aligned: 66
Modelled: 66
Confidence: 30.4%
Identity: 18%
PDB header:transferase
Chain: A: PDB Molecule:poly [adp-ribose] polymerase-1;
PDBTitle: solution structure of the second zn-finger domain of2 poly(adp-ribose) polymerase-1

Phyre2

PDB 2egh chain A

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 29.9%
Identity: 21%
PDB header:oxidoreductase
Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase2 complexed with a magnesium ion, nadph and fosmidomycin

Phyre2

PDB 1k5h chain B

3D model

Region: 397 - 435
Aligned: 39
Modelled: 39
Confidence: 29.0%
Identity: 21%
PDB header:oxidoreductase
Chain: B: PDB Molecule:1-deoxy-d-xylulose-5-phosphate reductoisomerase;
PDBTitle: 1-deoxy-d-xylulose-5-phosphate reductoisomerase

Phyre2
1
d1r9da_
2
c2y8nC_
3
c2f3oB_
4
d1h16a_
5
d1qhma_
6
d1hk8a_
7
c1hk8A_
8
d1qkra_
9
d1r0ka1
10
c3gr1A_
11
d1q0qa1
12
c2jcyA_
13
c3au9A_
14
c1r0lD_
15
c1v9xA_
16
c3odeA_
17
c3gr0D_
18
c2cs2A_
19
c2eghA_
20
c1k5hB_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
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41
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54
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63
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65
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1r9da_
100.0 38 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
2c2y8nC_
100.0 28 PDB header:lyase
Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit;
PDBTitle: crystal structure of glycyl radical enzyme
3c2f3oB_
100.0 32 PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus
4d1h16a_
100.0 26 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
5d1qhma_
100.0 22 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
6d1hk8a_
99.4 18 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
7c1hk8A_
99.4 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase;
PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp
8d1qkra_
71.1 24 Fold:Four-helical up-and-down bundle
Superfamily:alpha-catenin/vinculin-like
Family:alpha-catenin/vinculin
9d1r0ka1
63.9 28 Fold:Left-handed superhelix
Superfamily:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Family:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
10c3gr1A_
63.2 18 PDB header:membrane protein
Chain: A: PDB Molecule:protein prgh;
PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392)
11d1q0qa1
48.6 21 Fold:Left-handed superhelix
Superfamily:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
Family:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
12c2jcyA_
45.1 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis
13c3au9A_
44.5 23 PDB header:isomerase/isomerase inhibitor
Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: crystal structure of the quaternary complex-1 of an isomerase
14c1r0lD_
44.1 28 PDB header:oxidoreductase
Chain: D: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: 1-deoxy-d-xylulose 5-phosphate reductoisomerase from2 zymomonas mobilis in complex with nadph
15c1v9xA_
42.2 14 PDB header:transferase
Chain: A: PDB Molecule:poly (adp-ribose) polymerase;
PDBTitle: solution structure of the first zn-finger domain of2 poly(adp-ribose) polymerase-1
16c3odeA_
38.5 18 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1;
PDBTitle: human parp-1 zinc finger 2 (zn2) bound to dna
17c3gr0D_
32.4 18 PDB header:membrane protein
Chain: D: PDB Molecule:protein prgh;
PDBTitle: periplasmic domain of the t3ss inner membrane protein prgh from2 s.typhimurium (fragment 170-362)
18c2cs2A_
30.4 18 PDB header:transferase
Chain: A: PDB Molecule:poly [adp-ribose] polymerase-1;
PDBTitle: solution structure of the second zn-finger domain of2 poly(adp-ribose) polymerase-1
19c2eghA_
29.9 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase2 complexed with a magnesium ion, nadph and fosmidomycin
20c1k5hB_
29.0 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:1-deoxy-d-xylulose-5-phosphate reductoisomerase;
PDBTitle: 1-deoxy-d-xylulose-5-phosphate reductoisomerase
21c1aq5C_
not modelled 26.9 32 PDB header:coiled-coil
Chain: C: PDB Molecule:cartilage matrix protein;
PDBTitle: high-resolution solution nmr structure of the trimeric coiled-coil2 domain of chicken cartilage matrix protein, 20 structures
22c2f40A_
not modelled 25.9 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pf1455;
PDBTitle: structure of a novel protein from backbone-centered nmr data and nmr-2 assisted structure prediction
23c2dmjA_
not modelled 24.4 14 PDB header:transferase
Chain: A: PDB Molecule:poly (adp-ribose) polymerase family, member 1;
PDBTitle: solution structure of the first zf-parp domain of human2 poly(adp-ribose)polymerase-1
24d1vioa2
not modelled 24.3 18 Fold:Alpha-L RNA-binding motif
Superfamily:Alpha-L RNA-binding motif
Family:Pseudouridine synthase RsuA N-terminal domain
25d1jvaa3
not modelled 21.2 11 Fold:Homing endonuclease-like
Superfamily:Homing endonucleases
Family:Intein endonuclease
26c2z4tA_
not modelled 20.2 15 PDB header:transferase
Chain: A: PDB Molecule:beta-galactoside alpha-2,6-sialyltransferase;
PDBTitle: crystal structure of vibrionaceae photobacterium sp. jt-ish-224 2,6-2 sialyltransferase in a ternary complex with donor product cmp and3 accepter substrate lactose
27d1u5tb1
not modelled 19.6 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Vacuolar sorting protein domain
28d1v5ra1
not modelled 18.9 44 Fold:N domain of copper amine oxidase-like
Superfamily:GAS2 domain-like
Family:GAS2 domain
29d1p9ka_
not modelled 18.2 14 Fold:Alpha-L RNA-binding motif
Superfamily:Alpha-L RNA-binding motif
Family:YbcJ-like
30d2i9ia1
not modelled 17.7 20 Fold:Anticodon-binding domain-like
Superfamily:XCC0632-like
Family:NLBH-like
31c2i9iA_
not modelled 17.7 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of helicobacter pylori protein hp0492
32d1nh2a2
not modelled 17.3 21 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
33c2jobA_
not modelled 17.1 14 PDB header:lipid binding protein
Chain: A: PDB Molecule:antilipopolysaccharide factor;
PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site
34c1fuiB_
not modelled 16.9 20 PDB header:isomerase
Chain: B: PDB Molecule:l-fucose isomerase;
PDBTitle: l-fucose isomerase from escherichia coli
35d1pgja1
not modelled 16.7 27 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain
36d1aisa1
not modelled 16.5 9 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
37d1nh2a1
not modelled 16.5 17 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
38d1i36a1
not modelled 16.4 18 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:Conserved hypothetical protein MTH1747
39c2q01A_
not modelled 16.1 15 PDB header:isomerase
Chain: A: PDB Molecule:uronate isomerase;
PDBTitle: crystal structure of glucuronate isomerase from caulobacter crescentus
40d1qnaa2
not modelled 16.1 21 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
41d1irxa1
not modelled 15.8 13 Fold:An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Superfamily:An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Family:C-terminal domain of class I lysyl-tRNA synthetase
42d1r0ka3
not modelled 15.8 30 Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:Dihydrodipicolinate reductase-like
43d1mp9a1
not modelled 15.8 36 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
44d1aisa2
not modelled 15.6 33 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
45c2knjA_
not modelled 15.4 17 PDB header:antimicrobial protein
Chain: A: PDB Molecule:microplusin preprotein;
PDBTitle: nmr structure of microplusin a antimicrobial peptide from2 rhipicephalus (boophilus) microplus
46d2i15a1
not modelled 15.2 40 Fold:MG296-like
Superfamily:MG296-like
Family:MG296-like
47c3inpA_
not modelled 14.9 16 PDB header:isomerase
Chain: A: PDB Molecule:d-ribulose-phosphate 3-epimerase;
PDBTitle: 2.05 angstrom resolution crystal structure of d-ribulose-phosphate 3-2 epimerase from francisella tularensis.
48d1uj8a1
not modelled 14.7 12 Fold:Another 3-helical bundle
Superfamily:IscX-like
Family:IscX-like
49c3eagA_
not modelled 14.6 22 PDB header:ligase
Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamyl-meso-
PDBTitle: the crystal structure of udp-n-acetylmuramate:l-alanyl-gamma-d-2 glutamyl-meso-diaminopimelate ligase (mpl) from neisseria3 meningitides
50d1qnaa1
not modelled 14.4 17 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
51d1dq3a4
not modelled 14.4 19 Fold:Homing endonuclease-like
Superfamily:Homing endonucleases
Family:Intein endonuclease
52d1mp9a2
not modelled 14.3 33 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
53c2khvA_
not modelled 14.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phage integrase;
PDBTitle: solution nmr structure of protein nmul_a0922 from2 nitrosospira multiformis. northeast structural genomics3 consortium target nmr38b.
54d1rlfa_
not modelled 13.8 8 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ras-binding domain, RBD
55d1q5qh_
not modelled 13.4 18 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Proteasome subunits
56d1fi3a_
not modelled 13.3 8 Fold:Cytochrome c
Superfamily:Cytochrome c
Family:monodomain cytochrome c
57d1nj1a3
not modelled 13.3 17 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
58d1cdwa2
not modelled 13.3 16 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
59c3a14B_
not modelled 13.1 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase;
PDBTitle: crystal structure of dxr from thermotoga maritima, in complex with2 nadph
60d1rypi_
not modelled 12.9 19 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Proteasome subunits
61c1r8jB_
not modelled 12.9 26 PDB header:circadian clock protein
Chain: B: PDB Molecule:kaia;
PDBTitle: crystal structure of circadian clock protein kaia from2 synechococcus elongatus
62d2bm3a1
not modelled 12.9 17 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
63d1cdwa1
not modelled 12.8 17 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
64d1tyja1
not modelled 12.5 22 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
65d1yuaa2
not modelled 12.5 44 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Prokaryotic DNA topoisomerase I, a C-terminal fragment
66c3ol0C_
not modelled 12.3 17 PDB header:de novo protein
Chain: C: PDB Molecule:de novo designed monomer trefoil-fold sub-domain which
PDBTitle: crystal structure of monofoil-4p homo-trimer: de novo designed monomer2 trefoil-fold sub-domain which forms homo-trimer assembly
67c2b59A_
not modelled 12.3 17 PDB header:hydrolase/structural protein
Chain: A: PDB Molecule:cog1196: chromosome segregation atpases;
PDBTitle: the type ii cohesin dockerin complex
68c3d36B_
not modelled 12.2 13 PDB header:transferase/transferase inhibitor
Chain: B: PDB Molecule:sporulation kinase b;
PDBTitle: how to switch off a histidine kinase: crystal structure of2 geobacillus stearothermophilus kinb with the inhibitor sda
69d1ciia1
not modelled 12.2 28 Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
70c2vpmB_
not modelled 12.1 11 PDB header:ligase
Chain: B: PDB Molecule:trypanothione synthetase;
PDBTitle: trypanothione synthetase
71c3ghpA_
not modelled 12.1 26 PDB header:structural protein
Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b;
PDBTitle: structure of the second type ii cohesin module from the2 adaptor scaa scaffoldin of acetivibrio cellulolyticus3 (including long c-terminal linker)
72c3thgA_
not modelled 12.0 31 PDB header:protein binding
Chain: A: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase activase 1,
PDBTitle: crystal structure of the creosote rubisco activase c-domain
73c2a7oA_
not modelled 12.0 18 PDB header:transcription
Chain: A: PDB Molecule:huntingtin interacting protein b;
PDBTitle: solution structure of the hset2/hypb sri domain
74c2kwvA_
not modelled 11.9 36 PDB header:protein binding/signaling protein
Chain: A: PDB Molecule:dna polymerase iota;
PDBTitle: solution structure of ubm1 of murine polymerase iota in complex with2 ubiquitin
75d1w7pd1
not modelled 11.9 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Vacuolar sorting protein domain
76c3fnkA_
not modelled 11.6 26 PDB header:structural protein
Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b;
PDBTitle: crystal structure of the second type ii cohesin module from2 the cellulosomal adaptor scaa scaffoldin of acetivibrio3 cellulolyticus
77c1u57A_
not modelled 11.6 15 PDB header:viral protein
Chain: A: PDB Molecule:gag polyprotein;
PDBTitle: nmr structure of the (345-392)gag sequence from hiv-1
78c2hx6A_
not modelled 11.5 38 PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease;
PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb
79c3nzwH_
not modelled 11.3 19 PDB header:hydrolase/hydrolase inhibitor
Chain: H: PDB Molecule:proteasome component pup1;
PDBTitle: crystal structure of the yeast 20s proteasome in complex with 2b
80d1aoya_
not modelled 11.1 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
81d1zv9a1
not modelled 11.1 30 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
82c3vjjA_
not modelled 11.1 18 PDB header:viral protein
Chain: A: PDB Molecule:p9-1;
PDBTitle: crystal structure analysis of the p9-1
83c3oryA_
not modelled 11.1 14 PDB header:hydrolase
Chain: A: PDB Molecule:flap endonuclease 1;
PDBTitle: crystal structure of flap endonuclease 1 from hyperthermophilic2 archaeon desulfurococcus amylolyticus
84d1st6a7
not modelled 11.0 11 Fold:Four-helical up-and-down bundle
Superfamily:alpha-catenin/vinculin-like
Family:alpha-catenin/vinculin
85d1uw0a_
not modelled 10.9 9 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:PARP-type zinc finger
86c2i6lB_
not modelled 10.8 17 PDB header:transferase
Chain: B: PDB Molecule:mitogen-activated protein kinase 6;
PDBTitle: crystal structure of human mitogen activated protein kinase2 6 (mapk6)
87c2d2rA_
not modelled 10.8 14 PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: crystal structure of helicobacter pylori undecaprenyl pyrophosphate2 synthase
88d1hx8a1
not modelled 10.7 13 Fold:Spectrin repeat-like
Superfamily:GAT-like domain
Family:Phosphoinositide-binding clathrin adaptor, domain 2
89d2gykb1
not modelled 10.6 22 Fold:His-Me finger endonucleases
Superfamily:His-Me finger endonucleases
Family:HNH-motif
90d2g39a2
not modelled 10.6 20 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase alpha subunit-like
91c3ltiA_
not modelled 10.5 10 PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of the escherichia coli rna polymerase beta subunit2 beta2-betai4 domains
92c2fhgC_
not modelled 10.2 11 PDB header:hydrolase
Chain: C: PDB Molecule:proteasome, beta subunit;
PDBTitle: crystal structure of mycobacterial tuberculosis proteasome
93d2jb0b1
not modelled 10.0 17 Fold:His-Me finger endonucleases
Superfamily:His-Me finger endonucleases
Family:HNH-motif
94d1x9na2
not modelled 10.0 11 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:DNA ligase/mRNA capping enzyme postcatalytic domain
95c3kh0A_
not modelled 9.8 17 PDB header:signaling protein
Chain: A: PDB Molecule:ral guanine nucleotide dissociation stimulator;
PDBTitle: crystal structure of the ras-association (ra) domain of2 ralgds
96c7ceiB_
not modelled 9.8 18 PDB header:immune system
Chain: B: PDB Molecule:protein (colicin e7 immunity protein);
PDBTitle: the endonuclease domain of colicin e7 in complex with its inhibitor2 im7 protein
97d1r6oc1
not modelled 9.6 26 Fold:ClpS-like
Superfamily:ClpS-like
Family:Adaptor protein ClpS (YljA)
98d1sj8a2
not modelled 9.5 17 Fold:I/LWEQ domain
Superfamily:I/LWEQ domain
Family:I/LWEQ domain
99d1lfda_
not modelled 9.4 13 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ras-binding domain, RBD

Binding site prediction 

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

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


Phyre is for academic use only

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