Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A7B1
DateThu Jan 5 11:05:15 GMT 2012
Unique Job ID98789f2b846547f3

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1xdoB_
Top template information
PDB header:transferase
Chain: B: PDB Molecule:polyphosphate kinase;
PDBTitle: crystal structure of escherichia coli polyphosphate kinase
Confidence and coverage
Confidence:100.0% Coverage:100%
687 residues (100% 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  MGQEKLYIEKELSWLSFNERVLQEAADKSNPLIERMRFLGIYSNNLDEFYKVRFAELKRR
Secondary structure 
SS confidence 
Disorder  ???????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  IIISEEQGSNSHSRHLLGKIQSRVLKADQEFDGLYNELLLEMARNQIFLINERQLSVNQQ
Secondary structure 
SS confidence 
Disorder 
??????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  NWLRHYFKQYLRQHITPILINPDTDLVQFLKDDYTYLAVEIIRGDTIRYALLEIPSDKVP
Secondary structure 
SS confidence 
Disorder 
??
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  RFVNLPPEAPRRRKPMILLDNILRYCLDDIFKGFFDYDALNAYSMKMTRDAEYDLVHEME
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  ASLMELMSSSLKQRLTAEPVRFVYQRDMPNALVEVLREKLTISRYDSIVPGGRYHNFKDF
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  INFPNVGKANLVNKPLPRLRHIWFDKAQFRNGFDAIRERDVLLYYPYHTFEHVLELLRQA
Secondary structure 
SS confidence 
Disorder 
??????????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  SFDPSVLAIKINIYRVAKDSRIIDSMIHAAHNGKKVTVVVELQARFDEEANIHWAKRLTE
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  AGVHVIFSAPGLKIHAKLFLISRKENGEVVRYAHIGTGNFNEKTARLYTDYSLLTADARI
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  TNEVRRVFNFIENPYRPVTFDYLMVSPQNSRRLLYEMVDREIANAQQGLPSGITLKLNNL
Secondary structure 
SS confidence 
Disorder 
??
????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  VDKGLVDRLYAASSSGVPVNLLVRGMCSLIPNLEGISDNIRAISIVDRYLEHDRVYIFEN
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  GGDKKVYLSSADWMTRNIDYRIEVATPLLDPRLKQRVLDIIDILFSDTVKARYIDKELSN
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........670.........680........
Sequence  RYVPRGNRRKVRAQLAIYDYIKSLEQPE
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 1xdo chain B

3D model

Region: 2 - 688
Aligned: 687
Modelled: 687
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: B: PDB Molecule:polyphosphate kinase;
PDBTitle: crystal structure of escherichia coli polyphosphate kinase

Phyre2

PDB 2o8r chain A

3D model

Region: 3 - 686
Aligned: 640
Modelled: 663
Confidence: 100.0%
Identity: 38%
PDB header:transferase
Chain: A: PDB Molecule:polyphosphate kinase;
PDBTitle: crystal structure of polyphosphate kinase from2 porphyromonas gingivalis

Phyre2

PDB 1xdp chain A domain 4

3D model

Region: 502 - 688
Aligned: 187
Modelled: 187
Confidence: 100.0%
Identity: 100%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Polyphosphate kinase C-terminal domain

Phyre2

PDB 2o8r chain A domain 4

3D model

Region: 502 - 686
Aligned: 184
Modelled: 185
Confidence: 100.0%
Identity: 43%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Polyphosphate kinase C-terminal domain

Phyre2

PDB 2o8r chain A domain 3

3D model

Region: 313 - 501
Aligned: 182
Modelled: 189
Confidence: 100.0%
Identity: 39%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Polyphosphate kinase C-terminal domain

Phyre2

PDB 1xdp chain A domain 2

3D model

Region: 107 - 314
Aligned: 208
Modelled: 208
Confidence: 100.0%
Identity: 100%
Fold: PHP14-like
Superfamily: PHP14-like
Family: PPK middle domain-like

Phyre2

PDB 1xdp chain A domain 3

3D model

Region: 315 - 501
Aligned: 187
Modelled: 187
Confidence: 100.0%
Identity: 100%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Polyphosphate kinase C-terminal domain

Phyre2

PDB 2o8r chain A domain 2

3D model

Region: 107 - 313
Aligned: 181
Modelled: 186
Confidence: 100.0%
Identity: 30%
Fold: PHP14-like
Superfamily: PHP14-like
Family: PPK middle domain-like

Phyre2

PDB 1xdp chain A domain 1

3D model

Region: 2 - 106
Aligned: 105
Modelled: 105
Confidence: 100.0%
Identity: 100%
Fold: Spectrin repeat-like
Superfamily: PPK N-terminal domain-like
Family: PPK N-terminal domain-like

Phyre2

PDB 2o8r chain A domain 1

3D model

Region: 3 - 106
Aligned: 93
Modelled: 104
Confidence: 100.0%
Identity: 38%
Fold: Spectrin repeat-like
Superfamily: PPK N-terminal domain-like
Family: PPK N-terminal domain-like

Phyre2

PDB 3hsi chain C

3D model

Region: 342 - 650
Aligned: 278
Modelled: 296
Confidence: 99.9%
Identity: 17%
PDB header:transferase
Chain: C: PDB Molecule:phosphatidylserine synthase;
PDBTitle: crystal structure of phosphatidylserine synthase haemophilus2 influenzae rd kw20

Phyre2

PDB 1v0s chain A

3D model

Region: 380 - 646
Aligned: 246
Modelled: 263
Confidence: 99.9%
Identity: 20%
PDB header:hydrolase
Chain: A: PDB Molecule:phospholipase d;
PDBTitle: uninhibited form of phospholipase d from streptomyces sp.2 strain pmf

Phyre2

PDB 1byr chain A

3D model

Region: 342 - 497
Aligned: 142
Modelled: 156
Confidence: 99.4%
Identity: 15%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Nuclease

Phyre2

PDB 1v0w chain A domain 2

3D model

Region: 360 - 498
Aligned: 129
Modelled: 139
Confidence: 99.1%
Identity: 17%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Phospholipase D

Phyre2

PDB 1v0w chain A domain 1

3D model

Region: 360 - 494
Aligned: 127
Modelled: 135
Confidence: 99.0%
Identity: 14%
Fold: Phospholipase D/nuclease
Superfamily: Phospholipase D/nuclease
Family: Phospholipase D

Phyre2

PDB 2c1l chain A

3D model

Region: 484 - 655
Aligned: 146
Modelled: 149
Confidence: 92.3%
Identity: 16%
PDB header:hydrolase
Chain: A: PDB Molecule:restriction endonuclease;
PDBTitle: structure of the bfii restriction endonuclease

Phyre2

PDB 2yv2 chain A

3D model

Region: 353 - 432
Aligned: 76
Modelled: 80
Confidence: 91.5%
Identity: 21%
PDB header:ligase
Chain: A: PDB Molecule:succinyl-coa synthetase alpha chain;
PDBTitle: crystal structure of succinyl-coa synthetase alpha chain from2 aeropyrum pernix k1

Phyre2

PDB 1vb5 chain A

3D model

Region: 371 - 427
Aligned: 54
Modelled: 57
Confidence: 91.0%
Identity: 19%
Fold: NagB/RpiA/CoA transferase-like
Superfamily: NagB/RpiA/CoA transferase-like
Family: IF2B-like

Phyre2

PDB 3ecs chain D

3D model

Region: 372 - 427
Aligned: 53
Modelled: 56
Confidence: 89.5%
Identity: 25%
PDB header:translation
Chain: D: PDB Molecule:translation initiation factor eif-2b subunit
PDBTitle: crystal structure of human eif2b alpha

Phyre2

PDB 2csu chain A domain 2

3D model

Region: 353 - 428
Aligned: 68
Modelled: 76
Confidence: 87.9%
Identity: 15%
Fold: Flavodoxin-like
Superfamily: Succinyl-CoA synthetase domains
Family: Succinyl-CoA synthetase domains

Phyre2
1
c1xdoB_
2
c2o8rA_
3
d1xdpa4
4
d2o8ra4
5
d2o8ra3
6
d1xdpa2
7
d1xdpa3
8
d2o8ra2
9
d1xdpa1
10
d2o8ra1
11
c3hsiC_
12
c1v0sA_
13
d1byra_
14
d1v0wa2
15
d1v0wa1
16
c2c1lA_
17
c2yv2A_
18
d1vb5a_
19
c3ecsD_
20
d2csua2
21
22
23
24
25
26
27
28
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1xdoB_
100.0 100 PDB header:transferase
Chain: B: PDB Molecule:polyphosphate kinase;
PDBTitle: crystal structure of escherichia coli polyphosphate kinase
2c2o8rA_
100.0 38 PDB header:transferase
Chain: A: PDB Molecule:polyphosphate kinase;
PDBTitle: crystal structure of polyphosphate kinase from2 porphyromonas gingivalis
3d1xdpa4
100.0 100 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Polyphosphate kinase C-terminal domain
4d2o8ra4
100.0 43 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Polyphosphate kinase C-terminal domain
5d2o8ra3
100.0 39 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Polyphosphate kinase C-terminal domain
6d1xdpa2
100.0 100 Fold:PHP14-like
Superfamily:PHP14-like
Family:PPK middle domain-like
7d1xdpa3
100.0 100 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Polyphosphate kinase C-terminal domain
8d2o8ra2
100.0 30 Fold:PHP14-like
Superfamily:PHP14-like
Family:PPK middle domain-like
9d1xdpa1
100.0 100 Fold:Spectrin repeat-like
Superfamily:PPK N-terminal domain-like
Family:PPK N-terminal domain-like
10d2o8ra1
100.0 38 Fold:Spectrin repeat-like
Superfamily:PPK N-terminal domain-like
Family:PPK N-terminal domain-like
11c3hsiC_
99.9 17 PDB header:transferase
Chain: C: PDB Molecule:phosphatidylserine synthase;
PDBTitle: crystal structure of phosphatidylserine synthase haemophilus2 influenzae rd kw20
12c1v0sA_
99.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:phospholipase d;
PDBTitle: uninhibited form of phospholipase d from streptomyces sp.2 strain pmf
13d1byra_
99.4 15 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Nuclease
14d1v0wa2
99.1 17 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Phospholipase D
15d1v0wa1
99.0 14 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Phospholipase D
16c2c1lA_
92.3 16 PDB header:hydrolase
Chain: A: PDB Molecule:restriction endonuclease;
PDBTitle: structure of the bfii restriction endonuclease
17c2yv2A_
91.5 21 PDB header:ligase
Chain: A: PDB Molecule:succinyl-coa synthetase alpha chain;
PDBTitle: crystal structure of succinyl-coa synthetase alpha chain from2 aeropyrum pernix k1
18d1vb5a_
91.0 19 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
19c3ecsD_
89.5 25 PDB header:translation
Chain: D: PDB Molecule:translation initiation factor eif-2b subunit
PDBTitle: crystal structure of human eif2b alpha
20d2csua2
87.9 15 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
21d1eucb1
not modelled 87.7 29 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
22c2fpgA_
not modelled 86.9 20 PDB header:ligase
Chain: A: PDB Molecule:succinyl-coa ligase [gdp-forming] alpha-chain,
PDBTitle: crystal structure of pig gtp-specific succinyl-coa2 synthetase in complex with gdp
23c3a11D_
not modelled 86.2 28 PDB header:isomerase
Chain: D: PDB Molecule:translation initiation factor eif-2b, delta
PDBTitle: crystal structure of ribose-1,5-bisphosphate isomerase from2 thermococcus kodakaraensis kod1
24d1oi7a2
not modelled 85.9 16 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
25d1t9ka_
not modelled 85.7 18 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
26c3r2jC_
not modelled 84.8 27 PDB header:hydrolase
Chain: C: PDB Molecule:alpha/beta-hydrolase-like protein;
PDBTitle: crystal structure of pnc1 from l. infantum in complex with nicotinate
27d2nu7a2
not modelled 84.7 18 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
28c2yboA_
not modelled 84.7 17 PDB header:transferase
Chain: A: PDB Molecule:methyltransferase;
PDBTitle: the x-ray structure of the sam-dependent uroporphyrinogen2 iii methyltransferase nire from pseudomonas aeruginosa in3 complex with sah
29d1zj8a2
not modelled 84.6 20 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:Duplicated SiR/NiR-like domains 1 and 3
30d1t5oa_
not modelled 84.5 18 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
31d2a0ua1
not modelled 82.9 8 Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:IF2B-like
32c2nu8D_
not modelled 82.8 16 PDB header:ligase
Chain: D: PDB Molecule:succinyl-coa ligase [adp-forming] subunit alpha;
PDBTitle: c123at mutant of e. coli succinyl-coa synthetase
33c3mwdB_
not modelled 81.4 19 PDB header:transferase
Chain: B: PDB Molecule:atp-citrate synthase;
PDBTitle: truncated human atp-citrate lyase with citrate bound
34c2yvkA_
not modelled 81.3 12 PDB header:isomerase
Chain: A: PDB Molecule:methylthioribose-1-phosphate isomerase;
PDBTitle: crystal structure of 5-methylthioribose 1-phosphate2 isomerase product complex from bacillus subtilis
35c2csuB_
not modelled 80.8 15 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:457aa long hypothetical protein;
PDBTitle: crystal structure of ph0766 from pyrococcus horikoshii ot3
36c1yd6A_
not modelled 80.3 18 PDB header:dna binding protein
Chain: A: PDB Molecule:uvrc;
PDBTitle: crystal structure of the giy-yig n-terminal endonuclease2 domain of uvrc from bacillus caldotenax
37c3gbcA_
not modelled 78.9 22 PDB header:hydrolase
Chain: A: PDB Molecule:pyrazinamidase/nicotinamidas pnca;
PDBTitle: determination of the crystal structure of the pyrazinamidase from2 m.tuberculosis : a structure-function analysis for prediction3 resistance to pyrazinamide
38c1oi7A_
not modelled 78.8 16 PDB header:synthetase
Chain: A: PDB Molecule:succinyl-coa synthetase alpha chain;
PDBTitle: the crystal structure of succinyl-coa synthetase alpha2 subunit from thermus thermophilus
39d1s4da_
not modelled 78.8 17 Fold:Tetrapyrrole methylase
Superfamily:Tetrapyrrole methylase
Family:Tetrapyrrole methylase
40c1yd2A_
not modelled 77.8 33 PDB header:dna binding protein
Chain: A: PDB Molecule:uvrabc system protein c;
PDBTitle: crystal structure of the giy-yig n-terminal endonuclease domain of2 uvrc from thermotoga maritima: point mutant y19f bound to the3 catalytic divalent cation
41d2nu7b1
not modelled 75.6 30 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
42c2b34C_
not modelled 75.5 14 PDB header:hydrolase
Chain: C: PDB Molecule:mar1 ribonuclease;
PDBTitle: structure of mar1 ribonuclease from caenorhabditis elegans
43c3ndcB_
not modelled 73.4 22 PDB header:transferase
Chain: B: PDB Molecule:precorrin-4 c(11)-methyltransferase;
PDBTitle: crystal structure of precorrin-4 c11-methyltransferase from2 rhodobacter capsulatus
44c1nvmG_
not modelled 73.3 9 PDB header:lyase/oxidoreductase
Chain: G: PDB Molecule:4-hydroxy-2-oxovalerate aldolase;
PDBTitle: crystal structure of a bifunctional aldolase-dehydrogenase :2 sequestering a reactive and volatile intermediate
45c1zj8B_
not modelled 68.7 19 PDB header:oxidoreductase
Chain: B: PDB Molecule:probable ferredoxin-dependent nitrite reductase nira;
PDBTitle: structure of mycobacterium tuberculosis nira protein
46c1eucB_
not modelled 68.5 28 PDB header:ligase
Chain: B: PDB Molecule:succinyl-coa synthetase, beta chain;
PDBTitle: crystal structure of dephosphorylated pig heart, gtp-2 specific succinyl-coa synthetase
47d1jy1a1
not modelled 67.4 13 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Tyrosyl-DNA phosphodiesterase TDP1
48d1qzqa1
not modelled 67.1 13 Fold:Phospholipase D/nuclease
Superfamily:Phospholipase D/nuclease
Family:Tyrosyl-DNA phosphodiesterase TDP1
49d1euca2
not modelled 65.1 20 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
50d2akja2
not modelled 63.1 17 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:Duplicated SiR/NiR-like domains 1 and 3
51c1yzvA_
not modelled 63.0 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: hypothetical protein from trypanosoma cruzi
52d1vhna_
not modelled 62.3 16 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
53d1jpma1
not modelled 60.3 14 Fold:TIM beta/alpha-barrel
Superfamily:Enolase C-terminal domain-like
Family:D-glucarate dehydratase-like
54d1nvma2
not modelled 56.9 11 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:HMGL-like
55d2nu7a1
not modelled 56.3 24 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
56c2h0rD_
not modelled 55.9 19 PDB header:hydrolase
Chain: D: PDB Molecule:nicotinamidase;
PDBTitle: structure of the yeast nicotinamidase pnc1p
57c2rqmA_
not modelled 54.7 24 PDB header:chaperone
Chain: A: PDB Molecule:mesoderm development candidate 2;
PDBTitle: nmr solution structure of mesoderm development (mesd) - open2 conformation
58d1x9ga_
not modelled 53.7 9 Fold:Isochorismatase-like hydrolases
Superfamily:Isochorismatase-like hydrolases
Family:Isochorismatase-like hydrolases
59d1yaca_
not modelled 52.2 13 Fold:Isochorismatase-like hydrolases
Superfamily:Isochorismatase-like hydrolases
Family:Isochorismatase-like hydrolases
60c3d3kD_
not modelled 51.1 12 PDB header:protein binding
Chain: D: PDB Molecule:enhancer of mrna-decapping protein 3;
PDBTitle: crystal structure of human edc3p
61d1ebda2
not modelled 50.7 30 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
62c3kwpA_
not modelled 50.4 11 PDB header:transferase
Chain: A: PDB Molecule:predicted methyltransferase;
PDBTitle: crystal structure of putative methyltransferase from lactobacillus2 brevis
63d1im5a_
not modelled 50.1 17 Fold:Isochorismatase-like hydrolases
Superfamily:Isochorismatase-like hydrolases
Family:Isochorismatase-like hydrolases
64d1ve2a1
not modelled 48.8 15 Fold:Tetrapyrrole methylase
Superfamily:Tetrapyrrole methylase
Family:Tetrapyrrole methylase
65c2hxtA_
not modelled 47.7 25 PDB header:unknown function
Chain: A: PDB Molecule:l-fuconate dehydratase;
PDBTitle: crystal structure of l-fuconate dehydratase from xanthomonas2 campestris liganded with mg++ and d-erythronohydroxamate
66c2pjuD_
not modelled 47.5 19 PDB header:transcription
Chain: D: PDB Molecule:propionate catabolism operon regulatory protein;
PDBTitle: crystal structure of propionate catabolism operon2 regulatory protein prpr
67c1rr2A_
not modelled 46.7 13 PDB header:transferase
Chain: A: PDB Molecule:transcarboxylase 5s subunit;
PDBTitle: propionibacterium shermanii transcarboxylase 5s subunit bound to 2-2 ketobutyric acid
68c2nu9E_
not modelled 46.2 34 PDB header:ligase
Chain: E: PDB Molecule:succinyl-coa synthetase beta chain;
PDBTitle: c123at mutant of e. coli succinyl-coa synthetase2 orthorhombic crystal form
69d1va0a1
not modelled 45.8 17 Fold:Tetrapyrrole methylase
Superfamily:Tetrapyrrole methylase
Family:Tetrapyrrole methylase
70c2q5cA_
not modelled 45.7 13 PDB header:transcription
Chain: A: PDB Molecule:ntrc family transcriptional regulator;
PDBTitle: crystal structure of ntrc family transcriptional regulator from2 clostridium acetobutylicum
71d1dxla2
not modelled 45.1 20 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
72d1aoga2
not modelled 44.4 19 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
73c2wtaA_
not modelled 44.1 18 PDB header:hydrolase
Chain: A: PDB Molecule:nicotinamidase;
PDBTitle: acinetobacter baumanii nicotinamidase pyrazinamidease
74d1lvla2
not modelled 43.5 18 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
75d1mk0a_
not modelled 41.4 32 Fold:GIY-YIG endonuclease
Superfamily:GIY-YIG endonuclease
Family:GIY-YIG endonuclease
76c3dmyA_
not modelled 41.2 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:protein fdra;
PDBTitle: crystal structure of a predicated acyl-coa synthetase from e.coli
77d1v59a2
not modelled 41.1 25 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
78c1cbfA_
not modelled 40.8 17 PDB header:methyltransferase
Chain: A: PDB Molecule:cobalt-precorrin-4 transmethylase;
PDBTitle: the x-ray structure of a cobalamin biosynthetic enzyme, cobalt2 precorrin-4 methyltransferase, cbif
79d1cbfa_
not modelled 40.8 17 Fold:Tetrapyrrole methylase
Superfamily:Tetrapyrrole methylase
Family:Tetrapyrrole methylase
80c1nopB_
not modelled 39.2 13 PDB header:hydrolase/dna
Chain: B: PDB Molecule:tyrosyl-dna phosphodiesterase 1;
PDBTitle: crystal structure of human tyrosyl-dna phosphodiesterase2 (tdp1) in complex with vanadate, dna and a human3 topoisomerase i-derived peptide
81c3eegB_
not modelled 38.1 19 PDB header:transferase
Chain: B: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of a 2-isopropylmalate synthase from2 cytophaga hutchinsonii
82c2jlaD_
not modelled 37.8 57 PDB header:transferase
Chain: D: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene
PDBTitle: crystal structure of e.coli mend, 2-succinyl-5-enolpyruvyl-2 6-hydroxy-3-cyclohexadiene-1-carboxylate synthase - semet3 protein
83c1nu5A_
not modelled 37.7 29 PDB header:isomerase
Chain: A: PDB Molecule:chloromuconate cycloisomerase;
PDBTitle: crystal structure of pseudomonas sp. p51 chloromuconate lactonizing2 enzyme
84d2pjua1
not modelled 36.9 19 Fold:Chelatase-like
Superfamily:PrpR receptor domain-like
Family:PrpR receptor domain-like
85d1oi7a1
not modelled 36.8 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
86d1djqa2
not modelled 35.7 20 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:C-terminal domain of adrenodoxin reductase-like
87c2v4jA_
not modelled 35.5 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:sulfite reductase, dissimilatory-type subunit
PDBTitle: the crystal structure of desulfovibrio vulgaris2 dissimilatory sulfite reductase bound to dsrc provides3 novel insights into the mechanism of sulfate respiration
88c2akjA_
not modelled 35.2 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:ferredoxin--nitrite reductase, chloroplast;
PDBTitle: structure of spinach nitrite reductase
89d1oy0a_
not modelled 35.2 21 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Ketopantoate hydroxymethyltransferase PanB
90d3lada2
not modelled 33.4 21 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
91d2d59a1
not modelled 31.7 23 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
92d1ojta2
not modelled 31.2 19 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
93c2qvhB_
not modelled 30.6 13 PDB header:lyase
Chain: B: PDB Molecule:o-succinylbenzoate-coa synthase;
PDBTitle: crystal structure of o-succinylbenzoate synthase complexed with o-2 succinyl benzoate (osb)
94d1j2ra_
not modelled 30.4 9 Fold:Isochorismatase-like hydrolases
Superfamily:Isochorismatase-like hydrolases
Family:Isochorismatase-like hydrolases
95c3msyC_
not modelled 30.3 11 PDB header:isomerase
Chain: C: PDB Molecule:mandelate racemase/muconate lactonizing enzyme;
PDBTitle: crystal structure of mandelate racemase/muconate lactonizing enzyme2 from a marine actinobacterium
96c3ivuB_
not modelled 30.1 17 PDB header:transferase
Chain: B: PDB Molecule:homocitrate synthase, mitochondrial;
PDBTitle: homocitrate synthase lys4 bound to 2-og
97c2kglA_
not modelled 29.9 24 PDB header:chaperone
Chain: A: PDB Molecule:mesoderm development candidate 2;
PDBTitle: nmr solution structure of mesd
98c3ot4F_
not modelled 28.7 9 PDB header:hydrolase
Chain: F: PDB Molecule:putative isochorismatase;
PDBTitle: structure and catalytic mechanism of bordetella bronchiseptica nicf
99d1pjqa2
not modelled 28.5 16 Fold:Tetrapyrrole methylase
Superfamily:Tetrapyrrole methylase
Family:Tetrapyrrole methylase
100c2i9sA_
not modelled 27.5 22 PDB header:chaperone
Chain: A: PDB Molecule:mesoderm development candidate 2;
PDBTitle: the solution structure of the core of mesoderm development2 (mesd).
101c1sy7B_
not modelled 27.1 9 PDB header:oxidoreductase
Chain: B: PDB Molecule:catalase 1;
PDBTitle: crystal structure of the catalase-1 from neurospora crassa, native2 structure at 1.75a resolution.
102c2dc1A_
not modelled 27.1 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-aspartate dehydrogenase;
PDBTitle: crystal structure of l-aspartate dehydrogenase from2 hyperthermophilic archaeon archaeoglobus fulgidus
103d1lpfa2
not modelled 26.2 24 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
104d1d7ya2
not modelled 25.8 21 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
105c1vixA_
not modelled 25.4 15 PDB header:hydrolase
Chain: A: PDB Molecule:peptidase t;
PDBTitle: crystal structure of a putative peptidase t
106d3grsa2
not modelled 25.2 17 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
107d1r6wa1
not modelled 25.2 12 Fold:TIM beta/alpha-barrel
Superfamily:Enolase C-terminal domain-like
Family:D-glucarate dehydratase-like
108c2yv1A_
not modelled 25.1 16 PDB header:ligase
Chain: A: PDB Molecule:succinyl-coa ligase [adp-forming] subunit alpha;
PDBTitle: crystal structure of succinyl-coa synthetase alpha chain from2 methanocaldococcus jannaschii dsm 2661
109d1zpda2
not modelled 24.6 35 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
110d1t9ba2
not modelled 24.4 24 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Pyruvate oxidase and decarboxylase Pyr module
111c3bezC_
not modelled 24.4 27 PDB header:hydrolase
Chain: C: PDB Molecule:protease 4;
PDBTitle: crystal structure of escherichia coli signal peptide peptidase (sppa),2 semet crystals
112c1pjtB_
not modelled 23.9 16 PDB header:transferase/oxidoreductase/lyase
Chain: B: PDB Molecule:siroheme synthase;
PDBTitle: the structure of the ser128ala point-mutant variant of cysg,2 the multifunctional3 methyltransferase/dehydrogenase/ferrochelatase for4 siroheme synthesis
113c2frxD_
not modelled 23.8 5 PDB header:transferase
Chain: D: PDB Molecule:hypothetical protein yebu;
PDBTitle: crystal structure of yebu, a m5c rna methyltransferase from e.coli
114c3ewbX_
not modelled 23.3 23 PDB header:transferase
Chain: X: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of n-terminal domain of putative 2-2 isopropylmalate synthase from listeria monocytogenes
115d1onfa2
not modelled 23.2 9 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
116d1xhca2
not modelled 22.6 19 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD/NAD-linked reductases, N-terminal and central domains
117d1tuea_
not modelled 22.5 27 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Extended AAA-ATPase domain
118d1tzza1
not modelled 22.5 21 Fold:TIM beta/alpha-barrel
Superfamily:Enolase C-terminal domain-like
Family:D-glucarate dehydratase-like
119d2ax3a2
not modelled 22.5 21 Fold:YjeF N-terminal domain-like
Superfamily:YjeF N-terminal domain-like
Family:YjeF N-terminal domain-like
120d3c7bb2
not modelled 22.3 24 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:DsrA/DsrB N-terminal-domain-like

Binding site prediction 

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

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


Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
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