Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP33913
DateThu Jan 5 11:52:42 GMT 2012
Unique Job IDa1992bf12d987542

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2o7jA_
Top template information
PDB header:sugar binding protein
Chain: A: PDB Molecule:oligopeptide abc transporter, periplasmic
PDBTitle: the x-ray crystal structure of a thermophilic cellobiose2 binding protein bound with cellopentaose
Confidence and coverage
Confidence:100.0% Coverage: 84%
508 residues ( 84% 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  MIVRILLLFIALFTFGVQAQAIKESYAFAVLGEPRYAFNFNHFDYVNPAAPKGGQITLSA
Secondary structure 
SS confidence 
Disorder  ?
??????????????????????
?
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LGTFDNFNRYALRGNPGARTEQLYDTLFTTSDDEPGSYYPLIAESARYADDYSWVEVAIN
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  PRARFHDGSPITARDVEFTFQKFMTEGVPQFRLVYKGTTVKAIAPLTVRIELAKPGKEDM
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LSLFSLPVFPEKYWKDHKLSDPLATPPLASGPYRVTSWKMGQNIVYSRVKDYWAANLPVN
Secondary structure 
SS confidence 
Disorder 
????
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  RGRWNFDTIRYDYYLDDNVAFEAFKAGAFDLRMENDAKNWATRYTGKNFDKKYIIKDEQK
Secondary structure 
SS confidence 
Disorder 
?
?
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  NESAQDTRWLAFNIQRPVFSDRRVREAITLAFDFEWMNKALFYNAWSRTNSYFQNTEYAA
Secondary structure 
SS confidence 
Disorder  ??
????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  RNYPDAAELVLLAPMKKDLPSEVFTQIYQPPVSKGDGYDRDNLLKADKLLNEAGWVLKGQ
Secondary structure 
SS confidence 
Disorder  ???
?????
??????
?
?
??
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  QRVNATTGQPLSFELLLPASSNSQWVLPFQHSLQRLGINMDIRKVDNSQITNRMRSRDYD
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  MMPRVWRAMPWPSSDLQISWSSEYINSTYNAPGVQSPVIDSLINQIIAAQGNKEKLLPLG
Secondary structure 
SS confidence 
Disorder 
??
???
?
????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  RALDRVLTWNYYMLPMWYMAEDRLAWWDKFSQPAVRPIYSLGIDTWWYDVNKAAKLPSAS
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   ....
Sequence  KQGE
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 2o7j chain A

3D model

Region: 51 - 586
Aligned: 508
Modelled: 514
Confidence: 100.0%
Identity: 19%
PDB header:sugar binding protein
Chain: A: PDB Molecule:oligopeptide abc transporter, periplasmic
PDBTitle: the x-ray crystal structure of a thermophilic cellobiose2 binding protein bound with cellopentaose

Phyre2

PDB 1zty chain A

3D model

Region: 55 - 587
Aligned: 493
Modelled: 509
Confidence: 100.0%
Identity: 18%
PDB header:sugar binding protein, signaling protein
Chain: A: PDB Molecule:chitin oligosaccharide binding protein;
PDBTitle: crystal structure of the chitin oligasaccharide binding2 protein

Phyre2

PDB 1xoc chain A domain 1

3D model

Region: 49 - 590
Aligned: 492
Modelled: 495
Confidence: 100.0%
Identity: 21%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 2wok chain A

3D model

Region: 46 - 590
Aligned: 495
Modelled: 504
Confidence: 100.0%
Identity: 20%
PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:clavulanic acid biosynthesis oligopeptide
PDBTitle: clavulanic acid biosynthesis oligopeptide2 binding protein 2 complexed with bradykinin

Phyre2

PDB 1vr5 chain A domain 1

3D model

Region: 51 - 596
Aligned: 511
Modelled: 515
Confidence: 100.0%
Identity: 16%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 1zlq chain A domain 1

3D model

Region: 55 - 592
Aligned: 485
Modelled: 498
Confidence: 100.0%
Identity: 20%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 1dpe chain A

3D model

Region: 55 - 589
Aligned: 479
Modelled: 496
Confidence: 100.0%
Identity: 17%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3tpa chain A

3D model

Region: 55 - 589
Aligned: 478
Modelled: 484
Confidence: 100.0%
Identity: 18%
PDB header:heme binding protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: structure of hbpa2 from haemophilus parasuis

Phyre2

PDB 3m8u chain A

3D model

Region: 54 - 589
Aligned: 479
Modelled: 491
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: crystal structure of glutathione-binding protein a (gbpa) from2 haemophilus parasuis sh0165 in complex with glutathione disulfide3 (gssg)

Phyre2

PDB 1jet chain A

3D model

Region: 46 - 590
Aligned: 489
Modelled: 518
Confidence: 100.0%
Identity: 17%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3t66 chain A

3D model

Region: 55 - 583
Aligned: 464
Modelled: 489
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:nickel abc transporter (nickel-binding protein);
PDBTitle: crystal structure of nickel abc transporter from bacillus halodurans

Phyre2

PDB 3o9p chain A

3D model

Region: 52 - 588
Aligned: 479
Modelled: 510
Confidence: 100.0%
Identity: 14%
PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:periplasmic murein peptide-binding protein;
PDBTitle: the structure of the escherichia coli murein tripeptide binding2 protein mppa

Phyre2

PDB 1uqw chain A

3D model

Region: 55 - 589
Aligned: 474
Modelled: 491
Confidence: 100.0%
Identity: 18%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 2grv chain C

3D model

Region: 55 - 583
Aligned: 475
Modelled: 488
Confidence: 100.0%
Identity: 16%
PDB header:biosynthetic protein
Chain: C: PDB Molecule:lpqw;
PDBTitle: crystal structure of lpqw

Phyre2

PDB 3fto chain A

3D model

Region: 43 - 594
Aligned: 498
Modelled: 504
Confidence: 100.0%
Identity: 19%
PDB header:peptide binding protein
Chain: A: PDB Molecule:oligopeptide-binding protein oppa;
PDBTitle: crystal structure of oppa in a open conformation

Phyre2

PDB 3ry3 chain B

3D model

Region: 55 - 587
Aligned: 473
Modelled: 498
Confidence: 100.0%
Identity: 20%
PDB header:transport protein
Chain: B: PDB Molecule:putative solute-binding protein;
PDBTitle: putative solute-binding protein from yersinia pestis.

Phyre2

PDB 2d5w chain A

3D model

Region: 50 - 588
Aligned: 499
Modelled: 507
Confidence: 100.0%
Identity: 17%
PDB header:peptide binding protein
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: the crystal structure of oligopeptide binding protein from thermus2 thermophilus hb8 complexed with pentapeptide

Phyre2

PDB 3rqt chain A

3D model

Region: 53 - 585
Aligned: 459
Modelled: 489
Confidence: 100.0%
Identity: 17%
PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: 1.5 angstrom crystal structure of the complex of ligand binding2 component of abc-type import system from staphylococcus aureus with3 nickel and two histidines

Phyre2

PDB 3lvu chain B

3D model

Region: 304 - 558
Aligned: 252
Modelled: 255
Confidence: 100.0%
Identity: 35%
PDB header:transport protein
Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding protein;
PDBTitle: crystal structure of abc transporter, periplasmic substrate-binding2 protein spo2066 from silicibacter pomeroyi

Phyre2

PDB 3pam chain B

3D model

Region: 307 - 560
Aligned: 246
Modelled: 252
Confidence: 100.0%
Identity: 35%
PDB header:transport protein
Chain: B: PDB Molecule:transmembrane protein;
PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1

Phyre2
1
c2o7jA_
2
c1ztyA_
3
d1xoca1
4
c2wokA_
5
d1vr5a1
6
d1zlqa1
7
d1dpea_
8
c3tpaA_
9
c3m8uA_
10
d1jeta_
11
c3t66A_
12
c3o9pA_
13
d1uqwa_
14
c2grvC_
15
c3ftoA_
16
c3ry3B_
17
c2d5wA_
18
c3rqtA_
19
c3lvuB_
20
c3pamB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2o7jA_
100.0 19 PDB header:sugar binding protein
Chain: A: PDB Molecule:oligopeptide abc transporter, periplasmic
PDBTitle: the x-ray crystal structure of a thermophilic cellobiose2 binding protein bound with cellopentaose
2c1ztyA_
100.0 18 PDB header:sugar binding protein, signaling protein
Chain: A: PDB Molecule:chitin oligosaccharide binding protein;
PDBTitle: crystal structure of the chitin oligasaccharide binding2 protein
3d1xoca1
100.0 21 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
4c2wokA_
100.0 20 PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:clavulanic acid biosynthesis oligopeptide
PDBTitle: clavulanic acid biosynthesis oligopeptide2 binding protein 2 complexed with bradykinin
5d1vr5a1
100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
6d1zlqa1
100.0 20 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
7d1dpea_
100.0 17 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
8c3tpaA_
100.0 18 PDB header:heme binding protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: structure of hbpa2 from haemophilus parasuis
9c3m8uA_
100.0 18 PDB header:transport protein
Chain: A: PDB Molecule:heme-binding protein a;
PDBTitle: crystal structure of glutathione-binding protein a (gbpa) from2 haemophilus parasuis sh0165 in complex with glutathione disulfide3 (gssg)
10d1jeta_
100.0 17 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
11c3t66A_
100.0 18 PDB header:transport protein
Chain: A: PDB Molecule:nickel abc transporter (nickel-binding protein);
PDBTitle: crystal structure of nickel abc transporter from bacillus halodurans
12c3o9pA_
100.0 14 PDB header:peptide binding protein/peptide
Chain: A: PDB Molecule:periplasmic murein peptide-binding protein;
PDBTitle: the structure of the escherichia coli murein tripeptide binding2 protein mppa
13d1uqwa_
100.0 18 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
14c2grvC_
100.0 16 PDB header:biosynthetic protein
Chain: C: PDB Molecule:lpqw;
PDBTitle: crystal structure of lpqw
15c3ftoA_
100.0 19 PDB header:peptide binding protein
Chain: A: PDB Molecule:oligopeptide-binding protein oppa;
PDBTitle: crystal structure of oppa in a open conformation
16c3ry3B_
100.0 20 PDB header:transport protein
Chain: B: PDB Molecule:putative solute-binding protein;
PDBTitle: putative solute-binding protein from yersinia pestis.
17c2d5wA_
100.0 17 PDB header:peptide binding protein
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: the crystal structure of oligopeptide binding protein from thermus2 thermophilus hb8 complexed with pentapeptide
18c3rqtA_
100.0 17 PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: 1.5 angstrom crystal structure of the complex of ligand binding2 component of abc-type import system from staphylococcus aureus with3 nickel and two histidines
19c3lvuB_
100.0 35 PDB header:transport protein
Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding protein;
PDBTitle: crystal structure of abc transporter, periplasmic substrate-binding2 protein spo2066 from silicibacter pomeroyi
20c3pamB_
100.0 35 PDB header:transport protein
Chain: B: PDB Molecule:transmembrane protein;
PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1
21c3o6pA_
not modelled 100.0 19 PDB header:protein binding
Chain: A: PDB Molecule:peptide abc transporter, peptide-binding protein;
PDBTitle: crystal structure of peptide abc transporter, peptide-binding protein
22c3chgB_
not modelled 96.3 15 PDB header:ligand binding protein
Chain: B: PDB Molecule:glycine betaine-binding protein;
PDBTitle: the compatible solute-binding protein opuac from bacillus2 subtilis in complex with dmsa
23c3l6gA_
not modelled 95.8 12 PDB header:glycine betaine-binding protein
Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding
PDBTitle: crystal structure of lactococcal opuac in its open conformation
24c3tmgA_
not modelled 95.6 13 PDB header:transport protein
Chain: A: PDB Molecule:glycine betaine, l-proline abc transporter,
PDBTitle: crystal structure of glycine betaine, l-proline abc transporter,2 glycine/betaine/l-proline-binding protein (prox) from borrelia3 burgdorferi
25d1r9la_
not modelled 93.7 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
26c2rejA_
not modelled 93.2 12 PDB header:choline-binding protein
Chain: A: PDB Molecule:putative glycine betaine abc transporter protein;
PDBTitle: abc-transporter choline binding protein in unliganded semi-2 closed conformation
27d2p0la1
not modelled 92.6 17 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:LplA-like
28c3nohA_
not modelled 92.6 17 PDB header:peptide binding protein
Chain: A: PDB Molecule:putative peptide binding protein;
PDBTitle: crystal structure of a putative peptide binding protein (rumgna_00914)2 from ruminococcus gnavus atcc 29149 at 1.60 a resolution
29c3r6uA_
not modelled 87.8 9 PDB header:transport protein
Chain: A: PDB Molecule:choline-binding protein;
PDBTitle: crystal structure of choline binding protein opubc from bacillus2 subtilis
30d2fz5a1
not modelled 82.1 3 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
31c3k2dA_
not modelled 82.0 7 PDB header:immune system
Chain: A: PDB Molecule:abc-type metal ion transport system, periplasmic component;
PDBTitle: crystal structure of immunogenic lipoprotein a from vibrio vulnificus
32d1sw5a_
not modelled 81.5 7 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
33c3ir1F_
not modelled 80.7 11 PDB header:protein binding
Chain: F: PDB Molecule:outer membrane lipoprotein gna1946;
PDBTitle: crystal structure of lipoprotein gna1946 from neisseria2 meningitidis
34d1f4pa_
not modelled 79.6 9 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
35d2hfqa1
not modelled 77.9 15 Fold:NE1680-like
Superfamily:NE1680-like
Family:NE1680-like
36c2hfqA_
not modelled 77.9 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: nmr structure of protein ne1680 from nitrosomonas europaea:2 northeast structural genomics consortium target net5
37c3gxaA_
not modelled 77.7 11 PDB header:protein binding
Chain: A: PDB Molecule:outer membrane lipoprotein gna1946;
PDBTitle: crystal structure of gna1946
38d1ykga1
not modelled 77.3 9 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Cytochrome p450 reductase N-terminal domain-like
39c2uzhB_
not modelled 77.0 16 PDB header:lyase
Chain: B: PDB Molecule:2c-methyl-d-erythritol 2,4-cyclodiphosphate
PDBTitle: mycobacterium smegmatis 2c-methyl-d-erythritol-2,4-2 cyclodiphosphate synthase (ispf)
40d1b1ca_
not modelled 75.9 5 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Cytochrome p450 reductase N-terminal domain-like
41d5nula_
not modelled 74.0 6 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
42d1xs5a_
not modelled 73.1 7 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
43c3hlyA_
not modelled 71.3 4 PDB header:flavoprotein
Chain: A: PDB Molecule:flavodoxin-like domain;
PDBTitle: crystal structure of the flavodoxin-like domain from2 synechococcus sp q5mzp6_synp6 protein. northeast structural3 genomics consortium target snr135d.
44c3kzgB_
not modelled 70.1 11 PDB header:transport protein
Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding
PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila
45d1ja1a2
not modelled 69.5 5 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Cytochrome p450 reductase N-terminal domain-like
46c3f6sI_
not modelled 69.4 7 PDB header:electron transport
Chain: I: PDB Molecule:flavodoxin;
PDBTitle: desulfovibrio desulfuricans (atcc 29577) oxidized flavodoxin2 alternate conformers
47c3ombA_
not modelled 69.2 13 PDB header:transport protein
Chain: A: PDB Molecule:extracellular solute-binding protein, family 1;
PDBTitle: crystal structure of extracellular solute-binding protein from2 bifidobacterium longum subsp. infantis
48c2bpoA_
not modelled 68.8 8 PDB header:reductase
Chain: A: PDB Molecule:nadph-cytochrom p450 reductase;
PDBTitle: crystal structure of the yeast cpr triple mutant: d74g,2 y75f, k78a.
49d1ycga1
not modelled 64.8 8 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
50c3fniA_
not modelled 63.9 5 PDB header:oxidoreductase
Chain: A: PDB Molecule:putative diflavin flavoprotein a 3;
PDBTitle: crystal structure of a diflavin flavoprotein a3 (all3895) from nostoc2 sp., northeast structural genomics consortium target nsr431a
51c3n5lA_
not modelled 62.5 17 PDB header:transport protein
Chain: A: PDB Molecule:binding protein component of abc phosphonate transporter;
PDBTitle: crystal structure of a binding protein component of abc phosphonate2 transporter (pa3383) from pseudomonas aeruginosa at 1.97 a resolution
52d1bvyf_
not modelled 61.7 9 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
53c1bvyF_
not modelled 61.7 9 PDB header:oxidoreductase
Chain: F: PDB Molecule:protein (cytochrome p450 bm-3);
PDBTitle: complex of the heme and fmn-binding domains of the2 cytochrome p450(bm-3)
54c2rc9A_
not modelled 61.6 11 PDB header:membrane protein
Chain: A: PDB Molecule:glutamate [nmda] receptor subunit 3a;
PDBTitle: crystal structure of the nr3a ligand binding core complex with acpc at2 1.96 angstrom resolution
55c3pppA_
not modelled 61.3 11 PDB header:transport protein
Chain: A: PDB Molecule:glycine betaine/carnitine/choline-binding protein;
PDBTitle: structures of the substrate-binding protein provide insights into the2 multiple compatible solutes binding specificities of bacillus3 subtilis abc transporter opuc
56c2p3nB_
not modelled 60.5 17 PDB header:hydrolase
Chain: B: PDB Molecule:inositol-1-monophosphatase;
PDBTitle: thermotoga maritima impase tm1415
57d1iv3a_
not modelled 60.0 27 Fold:Bacillus chorismate mutase-like
Superfamily:IpsF-like
Family:IpsF-like
58c3kn3C_
not modelled 58.3 9 PDB header:transcription
Chain: C: PDB Molecule:putative periplasmic protein;
PDBTitle: crystal structure of lysr substrate binding domain (25-263) of2 putative periplasmic protein from wolinella succinogenes
59c2pmpA_
not modelled 56.6 25 PDB header:lyase
Chain: A: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase;
PDBTitle: structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from2 the isoprenoid biosynthetic pathway of arabidopsis thaliana
60c1j9zB_
not modelled 56.4 7 PDB header:oxidoreductase
Chain: B: PDB Molecule:nadph-cytochrome p450 reductase;
PDBTitle: cypor-w677g
61c3f0gA_
not modelled 56.3 12 PDB header:lyase
Chain: A: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase;
PDBTitle: co-crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate2 synthase with cmp
62d1e5da1
not modelled 56.2 7 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
63d1vh8a_
not modelled 55.9 14 Fold:Bacillus chorismate mutase-like
Superfamily:IpsF-like
Family:IpsF-like
64d1w55a2
not modelled 55.4 16 Fold:Bacillus chorismate mutase-like
Superfamily:IpsF-like
Family:IpsF-like
65d1t0aa_
not modelled 54.5 17 Fold:Bacillus chorismate mutase-like
Superfamily:IpsF-like
Family:IpsF-like
66c3hr4C_
not modelled 53.6 10 PDB header:oxidoreductase/metal binding protein
Chain: C: PDB Molecule:nitric oxide synthase, inducible;
PDBTitle: human inos reductase and calmodulin complex
67c3lr1A_
not modelled 50.3 11 PDB header:transport protein
Chain: A: PDB Molecule:tungstate abc transporter, periplasmic tungstate-
PDBTitle: the crystal structure of the tungstate abc transporter from2 geobacter sulfurreducens
68d1p99a_
not modelled 50.1 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
69c1p99A_
not modelled 50.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pg110;
PDBTitle: 1.7a crystal structure of protein pg110 from staphylococcus2 aureus
70d1gx1a_
not modelled 49.8 16 Fold:Bacillus chorismate mutase-like
Superfamily:IpsF-like
Family:IpsF-like
71d1vmea1
not modelled 49.6 8 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Flavodoxin-related
72c3re3B_
not modelled 49.0 18 PDB header:lyase
Chain: B: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase;
PDBTitle: crystal structure of 2-c-methyl-d-erythritol 2,4-cyclodiphosphate2 synthase from francisella tularensis
73d1xvya_
not modelled 48.1 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
74c3nbmA_
not modelled 47.8 13 PDB header:transferase
Chain: A: PDB Molecule:pts system, lactose-specific iibc components;
PDBTitle: the lactose-specific iib component domain structure of the2 phosphoenolpyruvate:carbohydrate phosphotransferase system (pts) from3 streptococcus pneumoniae.
75c3s83A_
not modelled 47.7 13 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
76d2a5sa1
not modelled 47.5 7 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
77d1twya_
not modelled 47.2 6 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
78c1twyG_
not modelled 47.2 6 PDB header:structural genomics, unknown function
Chain: G: PDB Molecule:abc transporter, periplasmic substrate-binding protein;
PDBTitle: crystal structure of an abc-type phosphate transport receptor from2 vibrio cholerae
79d1tlla2
not modelled 46.0 3 Fold:Flavodoxin-like
Superfamily:Flavoproteins
Family:Cytochrome p450 reductase N-terminal domain-like
80c2y7iB_
not modelled 43.1 5 PDB header:arginine-binding protein
Chain: B: PDB Molecule:stm4351;
PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351.
81c3r39A_
not modelled 43.1 11 PDB header:transport protein
Chain: A: PDB Molecule:putative periplasmic binding protein;
PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica
82d1nnfa_
not modelled 42.8 8 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
83c3muqB_
not modelled 42.0 11 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized conserved protein;
PDBTitle: the crystal structure of a conserved functionally unknown protein from2 vibrio parahaemolyticus rimd 2210633
84c2hnbA_
not modelled 41.8 5 PDB header:electron transport
Chain: A: PDB Molecule:protein mioc;
PDBTitle: solution structure of a bacterial holo-flavodoxin
85d1xc1a_
not modelled 41.6 12 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
86c2axoA_
not modelled 41.0 18 PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein atu2684;
PDBTitle: x-ray crystal structure of protein agr_c_4864 from agrobacterium2 tumefaciens. northeast structural genomics consortium target atr35.
87c2ylnA_
not modelled 39.7 9 PDB header:transport protein
Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein,
PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation
88c2f5xC_
not modelled 39.5 10 PDB header:transport protein
Chain: C: PDB Molecule:bugd;
PDBTitle: structure of periplasmic binding protein bugd
89d1wdna_
not modelled 39.4 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
90c2wc1A_
not modelled 39.0 5 PDB header:electron transport
Chain: A: PDB Molecule:flavodoxin;
PDBTitle: three-dimensional structure of the nitrogen fixation2 flavodoxin (niff) from rhodobacter capsulatus at 2.2 a
91c3g41A_
not modelled 37.7 9 PDB header:transport protein
Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding
PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae
92c3hn0A_
not modelled 36.5 7 PDB header:transport protein
Chain: A: PDB Molecule:nitrate transport protein;
PDBTitle: crystal structure of an abc transporter (bdi_1369) from2 parabacteroides distasonis at 1.75 a resolution
93c2q2aD_
not modelled 36.2 11 PDB header:transport protein
Chain: D: PDB Molecule:artj;
PDBTitle: crystal structures of the arginine-, lysine-, histidine-2 binding protein artj from the thermophilic bacterium3 geobacillus stearothermophilus
94c3k4uA_
not modelled 36.2 7 PDB header:transport protein
Chain: A: PDB Molecule:binding component of abc transporter;
PDBTitle: crystal structure of putative binding component of abc transporter2 from wolinella succinogenes dsm 1740 complexed with lysine
95d2f06a2
not modelled 36.0 27 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:BT0572-like
96c3b6nA_
not modelled 35.2 17 PDB header:lyase
Chain: A: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate
PDBTitle: crystal structure of 2c-methyl-d-erythritol 2,4-2 cyclodiphosphate synthase pv003920 from plasmodium vivax
97c2q9uB_
not modelled 34.6 11 PDB header:oxidoreductase
Chain: B: PDB Molecule:a-type flavoprotein;
PDBTitle: crystal structure of the flavodiiron protein from giardia2 intestinalis
98d1hsla_
not modelled 33.5 5 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
99c1vmeB_
not modelled 33.5 10 PDB header:electron transport
Chain: B: PDB Molecule:flavoprotein;
PDBTitle: crystal structure of flavoprotein (tm0755) from thermotoga maritima at2 1.80 a resolution
100c2x5dD_
not modelled 33.0 18 PDB header:transferase
Chain: D: PDB Molecule:probable aminotransferase;
PDBTitle: crystal structure of a probable aminotransferase from2 pseudomonas aeruginosa
101c3tqwA_
not modelled 32.5 13 PDB header:transport protein
Chain: A: PDB Molecule:methionine-binding protein;
PDBTitle: structure of a abc transporter, periplasmic substrate-binding protein2 from coxiella burnetii
102c2xx7B_
not modelled 32.5 17 PDB header:transport protein
Chain: B: PDB Molecule:glutamate receptor 2;
PDBTitle: crystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-2 (trifluoromethyl)-4,5,6,7-tetrahydro-1h-indazole in complex with3 the ligand binding domain of the rat glua2 receptor and glutamate4 at 2.2a resolution.
103c1w57A_
not modelled 32.2 15 PDB header:transferase
Chain: A: PDB Molecule:ispd/ispf bifunctional enzyme;
PDBTitle: structure of the bifunctional ispdf from campylobacter2 jejuni containing zn
104c3luuA_
not modelled 31.4 15 PDB header:biosynthetic protein
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of protein with unknown function which belongs to2 pfam duf971 family (afe_2189) from acidithiobacillus ferrooxidans3 atcc 23270 at 1.93 a resolution
105d1xvxa_
not modelled 31.1 13 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
106c3delC_
not modelled 31.1 5 PDB header:protein binding, transport protein
Chain: C: PDB Molecule:arginine binding protein;
PDBTitle: the structure of ct381, the arginine binding protein from the2 periplasm chlamydia trachomatis
107d2axoa1
not modelled 30.8 18 Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Atu2684-like
108d1pb7a_
not modelled 30.4 11 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
109c2l2qA_
not modelled 29.4 16 PDB header:transferase
Chain: A: PDB Molecule:pts system, cellobiose-specific iib component (cela);
PDBTitle: solution structure of cellobiose-specific phosphotransferase iib2 component protein from borrelia burgdorferi
110c2ek8A_
not modelled 29.1 6 PDB header:hydrolase
Chain: A: PDB Molecule:aminopeptidase;
PDBTitle: aminopeptidase from aneurinibacillus sp. strain am-1
111d1us5a_
not modelled 27.9 9 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
112c2gquA_
not modelled 27.1 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:udp-n-acetylenolpyruvylglucosamine reductase;
PDBTitle: crystal structure of udp-n-acetylenolpyruvylglucosamine2 reductase (murb) from thermus caldophilus
113c3i6vA_
not modelled 26.8 18 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic his/glu/gln/arg/opine family-binding protein;
PDBTitle: crystal structure of a periplasmic his/glu/gln/arg/opine family-2 binding protein from silicibacter pomeroyi in complex with lysine
114c2qpqC_
not modelled 26.1 12 PDB header:transport protein
Chain: C: PDB Molecule:protein bug27;
PDBTitle: structure of bug27 from bordetella pertussis
115d1lsta_
not modelled 25.7 7 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
116d1h3da1
not modelled 25.6 13 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
117c2ieeB_
not modelled 24.2 14 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:probable abc transporter extracellular-binding
PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574.
118c1q1kA_
not modelled 23.7 13 PDB header:transferase
Chain: A: PDB Molecule:atp phosphoribosyltransferase;
PDBTitle: structure of atp-phosphoribosyltransferase from e. coli complexed with2 pr-atp
119d1z7me1
not modelled 23.4 18 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
120c3uifA_
not modelled 23.4 19 PDB header:transport protein
Chain: A: PDB Molecule:sulfonate abc transporter, periplasmic sulfonate-binding
PDBTitle: crystal structure of putative sulfonate abc transporter, periplasmic2 sulfonate-binding protein ssua from methylobacillus flagellatus kt

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