Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP32674
DateThu Jan 5 11:50:01 GMT 2012
Unique Job ID1779802ba0ed5d29

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: 99%
757 residues ( 99% 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  MTNRISRLKTALFANTREISLERALLYTASHRQTEGEPVILRRAKATAYILEHVEISIRD
Secondary structure 
SS confidence 
Disorder  ??
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  EELIAGNRTVKPRAGIMSPEMDPYWLLKELDQFPTRPQDRFAISEEDKRIYREELFPYWE
Secondary structure 
SS confidence 
Disorder 
?
?
??
?????
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  KRSMKDFINGQMTDEVKAATNTQIFSINQTDKGQGHIIIDYPRLLNHGLGELVAQMQQHC
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  QQQPENHFYQAALLLLEASQKHILRYAELAETMAANCTDAQRREELLTIAEISRHNAQHK
Secondary structure 
SS confidence 
Disorder  ????
????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  PQTFWQACQLFWYMNIILQYESNASSLSLGRFDQYMLPFYQTSLTQGEDAAFLKELLESL
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  WVKCNDIVLLRSTSSARYFAGFPTGYTALLGGLTENGRSAVNVLSFLCLDAYQSVQLPQP
Secondary structure 
SS confidence 
Disorder 
??
?
?
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  NLGVRTNALIDTPFLMKTAETIRFGTGIPQIFNDEVVVPAFLNRGVSLEDARDYSVVGCV
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  ELSIPGRTYGLHDIAMFNLLKVMEICLHENEGNAALTYEGLLEQIRAKISHYITLMVEGS
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  NICDIGHRDWAPVPLLSSFISDCLEKGRDITDGGARYNFSGVQGIGIANLSDSLHALKGM
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  VFEQQRLSFDELLSVLKANFATPEGEKVRARLINRFEKYGNDIDEVDNISAELLRHYCKE
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  VEKYQNPRGGYFTPGSYTVSAHVPLGSVVGATPDGRFAGEQLADGGLSPMLGQDAQGPTA
Secondary structure 
SS confidence 
Disorder 
?
????
???
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  VLKSVSKLDNTLLSNGTLLNVKFTPATLEGEAGLRKLADFLRAFTQLKLQHIQFNVVNAD
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........730.........740.........750.........760.....
Sequence  TLREAQQRPQDYAGLVVRVAGYSAFFVELSKEIQDDIIRRTAHQL
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: 1 - 765
Aligned: 757
Modelled: 765
Confidence: 100.0%
Identity: 42%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 2y8n chain C

3D model

Region: 2 - 764
Aligned: 758
Modelled: 763
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: 3 - 765
Aligned: 753
Modelled: 763
Confidence: 100.0%
Identity: 38%
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: 50 - 764
Aligned: 652
Modelled: 689
Confidence: 100.0%
Identity: 24%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1qhm chain A

3D model

Region: 50 - 627
Aligned: 516
Modelled: 563
Confidence: 100.0%
Identity: 21%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1hk8 chain A

3D model

Region: 239 - 715
Aligned: 384
Modelled: 432
Confidence: 99.4%
Identity: 17%
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: 239 - 715
Aligned: 384
Modelled: 432
Confidence: 99.4%
Identity: 17%
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: 190 - 237
Aligned: 45
Modelled: 48
Confidence: 85.3%
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: 375 - 476
Aligned: 74
Modelled: 80
Confidence: 84.4%
Identity: 27%
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 1q0q chain A domain 1

3D model

Region: 375 - 478
Aligned: 76
Modelled: 82
Confidence: 83.0%
Identity: 17%
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 1rlr chain A domain 2

3D model

Region: 373 - 709
Aligned: 273
Modelled: 288
Confidence: 73.7%
Identity: 14%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: R1 subunit of ribonucleotide reductase, C-terminal domain

Phyre2

PDB 1r0l chain D

3D model

Region: 375 - 476
Aligned: 74
Modelled: 80
Confidence: 65.5%
Identity: 27%
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 2egh chain A

3D model

Region: 375 - 481
Aligned: 79
Modelled: 85
Confidence: 61.8%
Identity: 16%
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 1xje chain A

3D model

Region: 373 - 534
Aligned: 123
Modelled: 146
Confidence: 55.0%
Identity: 19%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleotide reductase, b12-dependent;
PDBTitle: structural mechanism of allosteric substrate specificity in a2 ribonucleotide reductase: dttp-gdp complex

Phyre2

PDB 1tt9 chain B

3D model

Region: 47 - 254
Aligned: 187
Modelled: 189
Confidence: 53.2%
Identity: 11%
PDB header:transferase, lyase
Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase
PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer

Phyre2

PDB 3gr1 chain A

3D model

Region: 674 - 716
Aligned: 39
Modelled: 43
Confidence: 51.8%
Identity: 10%
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 2d2r chain A

3D model

Region: 693 - 757
Aligned: 61
Modelled: 65
Confidence: 50.5%
Identity: 23%
PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: crystal structure of helicobacter pylori undecaprenyl pyrophosphate2 synthase

Phyre2

PDB 1u5t chain B domain 1

3D model

Region: 577 - 614
Aligned: 38
Modelled: 38
Confidence: 45.2%
Identity: 18%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Vacuolar sorting protein domain

Phyre2

PDB 1dq3 chain A domain 4

3D model

Region: 683 - 727
Aligned: 43
Modelled: 45
Confidence: 43.1%
Identity: 14%
Fold: Homing endonuclease-like
Superfamily: Homing endonucleases
Family: Intein endonuclease

Phyre2

PDB 1ueh chain A

3D model

Region: 691 - 757
Aligned: 64
Modelled: 67
Confidence: 42.6%
Identity: 9%
Fold: Undecaprenyl diphosphate synthase
Superfamily: Undecaprenyl diphosphate synthase
Family: Undecaprenyl diphosphate synthase

Phyre2
1
d1r9da_
2
c2y8nC_
3
c2f3oB_
4
d1h16a_
5
d1qhma_
6
d1hk8a_
7
c1hk8A_
8
d1qkra_
9
d1r0ka1
10
d1q0qa1
11
d1rlra2
12
c1r0lD_
13
c2eghA_
14
c1xjeA_
15
c1tt9B_
16
c3gr1A_
17
c2d2rA_
18
d1u5tb1
19
d1dq3a4
20
d1ueha_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
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36
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46
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1r9da_
100.0 42 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 38 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 24 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
5d1qhma_
100.0 21 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
6d1hk8a_
99.4 17 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
7c1hk8A_
99.4 17 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_
85.3 24 Fold:Four-helical up-and-down bundle
Superfamily:alpha-catenin/vinculin-like
Family:alpha-catenin/vinculin
9d1r0ka1
84.4 27 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
10d1q0qa1
83.0 17 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
11d1rlra2
73.7 14 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
12c1r0lD_
65.5 27 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
13c2eghA_
61.8 16 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
14c1xjeA_
55.0 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleotide reductase, b12-dependent;
PDBTitle: structural mechanism of allosteric substrate specificity in a2 ribonucleotide reductase: dttp-gdp complex
15c1tt9B_
53.2 11 PDB header:transferase, lyase
Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase
PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer
16c3gr1A_
51.8 10 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)
17c2d2rA_
50.5 23 PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: crystal structure of helicobacter pylori undecaprenyl pyrophosphate2 synthase
18d1u5tb1
45.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Vacuolar sorting protein domain
19d1dq3a4
43.1 14 Fold:Homing endonuclease-like
Superfamily:Homing endonucleases
Family:Intein endonuclease
20d1ueha_
42.6 9 Fold:Undecaprenyl diphosphate synthase
Superfamily:Undecaprenyl diphosphate synthase
Family:Undecaprenyl diphosphate synthase
21d2gykb1
not modelled 41.9 12 Fold:His-Me finger endonucleases
Superfamily:His-Me finger endonucleases
Family:HNH-motif
22d1jvaa3
not modelled 41.8 11 Fold:Homing endonuclease-like
Superfamily:Homing endonucleases
Family:Intein endonuclease
23c2jcyA_
not modelled 39.7 22 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
24c1jp3A_
not modelled 39.1 11 PDB header:transferase
Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: structure of e.coli undecaprenyl pyrophosphate synthase
25c1k5hB_
not modelled 37.4 17 PDB header:oxidoreductase
Chain: B: PDB Molecule:1-deoxy-d-xylulose-5-phosphate reductoisomerase;
PDBTitle: 1-deoxy-d-xylulose-5-phosphate reductoisomerase
26c1rh1A_
not modelled 33.3 11 PDB header:antibiotic
Chain: A: PDB Molecule:colicin b;
PDBTitle: crystal structure of the cytotoxic bacterial protein2 colicin b at 2.5 a resolution
27d1st6a7
not modelled 32.3 8 Fold:Four-helical up-and-down bundle
Superfamily:alpha-catenin/vinculin-like
Family:alpha-catenin/vinculin
28c3au9A_
not modelled 31.9 14 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
29c2vg2C_
not modelled 29.3 17 PDB header:transferase
Chain: C: PDB Molecule:undecaprenyl pyrophosphate synthetase;
PDBTitle: rv2361 with ipp
30c3odeA_
not modelled 26.4 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
31c1v9xA_
not modelled 25.9 16 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
32d1fi3a_
not modelled 25.6 13 Fold:Cytochrome c
Superfamily:Cytochrome c
Family:monodomain cytochrome c
33c2f40A_
not modelled 25.4 29 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
34d1f75a_
not modelled 23.4 16 Fold:Undecaprenyl diphosphate synthase
Superfamily:Undecaprenyl diphosphate synthase
Family:Undecaprenyl diphosphate synthase
35d1nh2a2
not modelled 22.7 29 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
36c3gr0D_
not modelled 22.6 12 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)
37c3thgA_
not modelled 22.5 29 PDB header:protein binding
Chain: A: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase activase 1,
PDBTitle: crystal structure of the creosote rubisco activase c-domain
38c3ajfA_
not modelled 21.6 27 PDB header:viral protein
Chain: A: PDB Molecule:non-structural protein 3;
PDBTitle: structural insigths into dsrna binding and rna silencing suppression2 by ns3 protein of rice hoja blanca tenuivirus
39c2dmjA_
not modelled 21.6 11 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
40d1mp9a1
not modelled 21.5 29 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
41d1nh2a1
not modelled 21.4 25 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
42d1l1la_
not modelled 21.3 19 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:B12-dependent (class II) ribonucleotide reductase
43d1qnaa2
not modelled 21.2 29 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
44d1aisa1
not modelled 20.9 18 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
45d1vioa2
not modelled 20.9 12 Fold:Alpha-L RNA-binding motif
Superfamily:Alpha-L RNA-binding motif
Family:Pseudouridine synthase RsuA N-terminal domain
46d1rlfa_
not modelled 20.3 13 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ras-binding domain, RBD
47d1aisa2
not modelled 20.0 29 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
48d1pugb_
not modelled 19.6 26 Fold:YbaB-like
Superfamily:YbaB-like
Family:YbaB-like
49d1qnaa1
not modelled 19.5 21 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
50d1v5ra1
not modelled 18.9 44 Fold:N domain of copper amine oxidase-like
Superfamily:GAS2 domain-like
Family:GAS2 domain
51d2i15a1
not modelled 18.7 30 Fold:MG296-like
Superfamily:MG296-like
Family:MG296-like
52c1fuiB_
not modelled 18.6 21 PDB header:isomerase
Chain: B: PDB Molecule:l-fucose isomerase;
PDBTitle: l-fucose isomerase from escherichia coli
53c2cvuA_
not modelled 18.5 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i
54d1mp9a2
not modelled 18.2 29 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
55c3hnfA_
not modelled 17.7 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large subunit;
PDBTitle: crystal structure of human ribonucleotide reductase 1 bound to the2 effectors ttp and datp
56c3mf2B_
not modelled 17.5 17 PDB header:ligase
Chain: B: PDB Molecule:bll0957 protein;
PDBTitle: crystal structure of class ii aars homologue (bll0957) complexed with2 amp
57d351ca_
not modelled 17.3 8 Fold:Cytochrome c
Superfamily:Cytochrome c
Family:monodomain cytochrome c
58d2g39a2
not modelled 17.2 23 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:CoA transferase alpha subunit-like
59d1cdwa1
not modelled 17.0 25 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
60c3inpA_
not modelled 17.0 22 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.
61d1lfda_
not modelled 16.7 17 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ras-binding domain, RBD
62d2bm3a1
not modelled 16.2 29 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
63c3kh0A_
not modelled 16.2 22 PDB header:signaling protein
Chain: A: PDB Molecule:ral guanine nucleotide dissociation stimulator;
PDBTitle: crystal structure of the ras-association (ra) domain of2 ralgds
64d1tyja1
not modelled 15.6 29 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
65d1uj8a1
not modelled 15.5 24 Fold:Another 3-helical bundle
Superfamily:IscX-like
Family:IscX-like
66c2b59A_
not modelled 15.5 29 PDB header:hydrolase/structural protein
Chain: A: PDB Molecule:cog1196: chromosome segregation atpases;
PDBTitle: the type ii cohesin dockerin complex
67c2cs2A_
not modelled 15.4 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
68c3hp7A_
not modelled 15.3 29 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hemolysin, putative;
PDBTitle: putative hemolysin from streptococcus thermophilus.
69d1cdwa2
not modelled 15.1 21 Fold:TBP-like
Superfamily:TATA-box binding protein-like
Family:TATA-box binding protein (TBP), C-terminal domain
70c3rmrA_
not modelled 15.0 23 PDB header:protein binding
Chain: A: PDB Molecule:avirulence protein;
PDBTitle: crystal structure of hyaloperonospora arabidopsidis atr1 effector2 domain
71c2jobA_
not modelled 15.0 15 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
72c3ugsB_
not modelled 14.9 11 PDB header:transferase
Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase;
PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni
73d1ynra1
not modelled 14.9 13 Fold:Cytochrome c
Superfamily:Cytochrome c
Family:monodomain cytochrome c
74d1rypi_
not modelled 14.8 19 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Proteasome subunits
75c3ol0C_
not modelled 14.6 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
76d2rgfa_
not modelled 14.5 22 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ras-binding domain, RBD
77c3fnkA_
not modelled 14.5 36 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
78c3ghpA_
not modelled 14.4 36 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)
79d1q5qh_
not modelled 14.0 6 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Proteasome subunits
80c3oryA_
not modelled 14.0 19 PDB header:hydrolase
Chain: A: PDB Molecule:flap endonuclease 1;
PDBTitle: crystal structure of flap endonuclease 1 from hyperthermophilic2 archaeon desulfurococcus amylolyticus
81d1lghb_
not modelled 14.0 5 Fold:Light-harvesting complex subunits
Superfamily:Light-harvesting complex subunits
Family:Light-harvesting complex subunits
82c2wghA_
not modelled 14.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large
PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg.
83c2vpmB_
not modelled 13.9 17 PDB header:ligase
Chain: B: PDB Molecule:trypanothione synthetase;
PDBTitle: trypanothione synthetase
84d1irxa1
not modelled 13.9 14 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
85d1yuaa2
not modelled 13.8 56 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Prokaryotic DNA topoisomerase I, a C-terminal fragment
86d1zv9a1
not modelled 13.5 50 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
87d1twda_
not modelled 13.5 26 Fold:TIM beta/alpha-barrel
Superfamily:CutC-like
Family:CutC-like
88d1nj1a3
not modelled 13.5 15 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
89c2qguA_
not modelled 13.2 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:probable signal peptide protein;
PDBTitle: three-dimensional structure of the phospholipid-binding protein from2 ralstonia solanacearum q8xv73_ralsq in complex with a phospholipid at3 the resolution 1.53 a. northeast structural genomics consortium4 target rsr89
90c3nzwH_
not modelled 13.0 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
91d1xppa_
not modelled 12.9 10 Fold:DCoH-like
Superfamily:RBP11-like subunits of RNA polymerase
Family:RBP11/RpoL
92c2kwvA_
not modelled 12.6 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
93c3eagA_
not modelled 12.6 14 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
94d1i36a1
not modelled 12.5 16 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:Conserved hypothetical protein MTH1747
95c3a14B_
not modelled 12.1 27 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
96d1w7pd1
not modelled 12.1 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Vacuolar sorting protein domain
97d1zsqa2
not modelled 12.0 18 Fold:(Phosphotyrosine protein) phosphatases II
Superfamily:(Phosphotyrosine protein) phosphatases II
Family:Myotubularin-like phosphatases
98d1seda_
not modelled 12.0 9 Fold:Hypothetical protein YhaI
Superfamily:Hypothetical protein YhaI
Family:Hypothetical protein YhaI
99c2hx6A_
not modelled 11.9 38 PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease;
PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb

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