Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP27253
DateThu Jan 5 11:43:33 GMT 2012
Unique Job IDe9a796d14d3bb0a9

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1e1cA_
Top template information
PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant
Confidence and coverage
Confidence:100.0% Coverage: 98%
700 residues ( 98% 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  MSNVQEWQQLANKELSRREKTVDSLVHQTAEGIAIKPLYTEADLDNLEVTGTLPGLPPYV
Secondary structure 
SS confidence 
Disorder  ???
??
?????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  RGPRATMYTAQPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLATHRGYDSDNPR
Secondary structure 
SS confidence 
Disorder 
?????????
?????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  VAGDVGKAGVAIDTVEDMKVLFDQIPLDKMSVSMTMNGAVLPVLAFYIVAAEEQGVTPDK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LTGTIQNDILKEYLCRNTYIYPPKPSMRIIADIIAWCSGNMPRFNTISISGYHMGEAGAN
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  CVQQVAFTLADGIEYIKAAISAGLKIDDFAPRLSFFFGIGMDLFMNVAMLRAARYLWSEA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  VSGFGAQDPKSLALRTHCQTSGWSLTEQDPYNNVIRTTIEALAATLGGTQSLHTNAFDEA
Secondary structure 
SS confidence 
Disorder 
???
??
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  LGLPTDFSARIARNTQIIIQEESELCRTVDPLAGSYYIESLTDQIVKQARAIIQQIDEAG
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  GMAKAIEAGLPKRMIEEASAREQSLIDQGKRVIVGVNKYKLDHEDETDVLEIDNVMVRNE
Secondary structure 
SS confidence 
Disorder 
???
?????????
???????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  QIASLERIRATRDDAAVTAALNALTHAAQHNENLLAAAVNAARVRATLGEISDALEVAFD
Secondary structure 
SS confidence 
Disorder 
?
??
?
??
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  RYLVPSQCVTGVIAQSYHQSEKSASEFDAIVAQTEQFLADNGRRPRILIAKMGQDGHDRG
Secondary structure 
SS confidence 
Disorder 
????
???
????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  AKVIASAYSDLGFDVDLSPMFSTPEEIARLAVENDVHVVGASSLAAGHKTLIPELVEALK
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........670.........680.........690.........700.........710....
Sequence  KWGREDICVVAGGVIPPQDYAFLQERGVAAIYGPGTPMLDSVRDVLNLISQHHD
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 1e1c chain A

3D model

Region: 3 - 714
Aligned: 700
Modelled: 708
Confidence: 100.0%
Identity: 58%
PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant

Phyre2

PDB 3bic chain A

3D model

Region: 3 - 712
Aligned: 697
Modelled: 710
Confidence: 100.0%
Identity: 58%
PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase, mitochondrial precursor;
PDBTitle: crystal structure of human methylmalonyl-coa mutase

Phyre2

PDB 6req chain B

3D model

Region: 2 - 709
Aligned: 593
Modelled: 604
Confidence: 100.0%
Identity: 27%
PDB header:isomerase
Chain: B: PDB Molecule:protein (methylmalonyl-coa mutase);
PDBTitle: methylmalonyl-coa mutase, 3-carboxypropyl-coa inhibitor complex

Phyre2

PDB 7req chain A domain 1

3D model

Region: 3 - 542
Aligned: 533
Modelled: 540
Confidence: 100.0%
Identity: 62%
Fold: TIM beta/alpha-barrel
Superfamily: Cobalamin (vitamin B12)-dependent enzymes
Family: Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Phyre2

PDB 7req chain B domain 1

3D model

Region: 2 - 468
Aligned: 436
Modelled: 440
Confidence: 100.0%
Identity: 26%
Fold: TIM beta/alpha-barrel
Superfamily: Cobalamin (vitamin B12)-dependent enzymes
Family: Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Phyre2

PDB 7req chain B domain 2

3D model

Region: 546 - 709
Aligned: 158
Modelled: 164
Confidence: 100.0%
Identity: 16%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 7req chain A domain 2

3D model

Region: 535 - 714
Aligned: 165
Modelled: 165
Confidence: 100.0%
Identity: 53%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1ccw chain A

3D model

Region: 583 - 712
Aligned: 130
Modelled: 130
Confidence: 99.6%
Identity: 25%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1xrs chain B domain 1

3D model

Region: 567 - 711
Aligned: 140
Modelled: 145
Confidence: 99.5%
Identity: 24%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1xrs chain B

3D model

Region: 567 - 711
Aligned: 140
Modelled: 145
Confidence: 99.5%
Identity: 24%
PDB header:isomerase
Chain: B: PDB Molecule:d-lysine 5,6-aminomutase beta subunit;
PDBTitle: crystal structure of lysine 5,6-aminomutase in complex with plp,2 cobalamin, and 5'-deoxyadenosine

Phyre2

PDB 2yxb chain A

3D model

Region: 583 - 712
Aligned: 129
Modelled: 130
Confidence: 99.4%
Identity: 42%
PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix

Phyre2

PDB 3kox chain A

3D model

Region: 9 - 711
Aligned: 649
Modelled: 684
Confidence: 99.4%
Identity: 17%
PDB header:metal binding protein
Chain: A: PDB Molecule:d-ornithine aminomutase e component;
PDBTitle: crystal structure of ornithine 4,5 aminomutase in complex with 2,4-2 diaminobutyrate (anaerobic)

Phyre2

PDB 1fmf chain A

3D model

Region: 583 - 709
Aligned: 127
Modelled: 127
Confidence: 99.1%
Identity: 24%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1y80 chain A

3D model

Region: 583 - 706
Aligned: 122
Modelled: 124
Confidence: 99.1%
Identity: 22%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica

Phyre2

PDB 1bmt chain B

3D model

Region: 487 - 707
Aligned: 207
Modelled: 221
Confidence: 99.0%
Identity: 18%
PDB header:methyltransferase
Chain: B: PDB Molecule:methionine synthase;
PDBTitle: how a protein binds b12: a 3.o angstrom x-ray structure of2 the b12-binding domains of methionine synthase

Phyre2

PDB 2i2x chain D

3D model

Region: 454 - 711
Aligned: 229
Modelled: 246
Confidence: 98.9%
Identity: 16%
PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri

Phyre2

PDB 1ccw chain B

3D model

Region: 75 - 431
Aligned: 318
Modelled: 344
Confidence: 98.9%
Identity: 19%
Fold: TIM beta/alpha-barrel
Superfamily: Cobalamin (vitamin B12)-dependent enzymes
Family: Glutamate mutase, large subunit

Phyre2

PDB 3ezx chain A

3D model

Region: 479 - 706
Aligned: 198
Modelled: 200
Confidence: 98.8%
Identity: 15%
PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein

Phyre2

PDB 3bul chain A domain 2

3D model

Region: 580 - 712
Aligned: 133
Modelled: 133
Confidence: 98.7%
Identity: 17%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1k98 chain A

3D model

Region: 487 - 712
Aligned: 212
Modelled: 226
Confidence: 98.5%
Identity: 19%
PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment

Phyre2
1
c1e1cA_
2
c3bicA_
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c6reqB_
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d7reqa1
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d7reqb1
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d7reqb2
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d7reqa2
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d1ccwa_
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d1xrsb1
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c1xrsB_
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c2yxbA_
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c3koxA_
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d1fmfa_
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c1y80A_
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c1bmtB_
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c2i2xD_
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d1ccwb_
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c3ezxA_
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d3bula2
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c1k98A_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1e1cA_
100.0 58 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant
2c3bicA_
100.0 58 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase, mitochondrial precursor;
PDBTitle: crystal structure of human methylmalonyl-coa mutase
3c6reqB_
100.0 27 PDB header:isomerase
Chain: B: PDB Molecule:protein (methylmalonyl-coa mutase);
PDBTitle: methylmalonyl-coa mutase, 3-carboxypropyl-coa inhibitor complex
4d7reqa1
100.0 62 Fold:TIM beta/alpha-barrel
Superfamily:Cobalamin (vitamin B12)-dependent enzymes
Family:Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain
5d7reqb1
100.0 26 Fold:TIM beta/alpha-barrel
Superfamily:Cobalamin (vitamin B12)-dependent enzymes
Family:Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain
6d7reqb2
100.0 16 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
7d7reqa2
100.0 53 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
8d1ccwa_
99.6 25 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
9d1xrsb1
99.5 24 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
10c1xrsB_
99.5 24 PDB header:isomerase
Chain: B: PDB Molecule:d-lysine 5,6-aminomutase beta subunit;
PDBTitle: crystal structure of lysine 5,6-aminomutase in complex with plp,2 cobalamin, and 5'-deoxyadenosine
11c2yxbA_
99.4 42 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
12c3koxA_
99.4 17 PDB header:metal binding protein
Chain: A: PDB Molecule:d-ornithine aminomutase e component;
PDBTitle: crystal structure of ornithine 4,5 aminomutase in complex with 2,4-2 diaminobutyrate (anaerobic)
13d1fmfa_
99.1 24 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
14c1y80A_
99.1 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica
15c1bmtB_
99.0 18 PDB header:methyltransferase
Chain: B: PDB Molecule:methionine synthase;
PDBTitle: how a protein binds b12: a 3.o angstrom x-ray structure of2 the b12-binding domains of methionine synthase
16c2i2xD_
98.9 16 PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri
17d1ccwb_
98.9 19 Fold:TIM beta/alpha-barrel
Superfamily:Cobalamin (vitamin B12)-dependent enzymes
Family:Glutamate mutase, large subunit
18c3ezxA_
98.8 15 PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein
19d3bula2
98.7 17 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
20c1k98A_
98.5 19 PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment
21c1zfjA_
not modelled 95.6 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine monophosphate dehydrogenase;
PDBTitle: inosine monophosphate dehydrogenase (impdh; ec 1.1.1.205) from2 streptococcus pyogenes
22d1krwa_
not modelled 95.6 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
23c1ys7B_
not modelled 95.6 18 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulatory protein prra;
PDBTitle: crystal structure of the response regulator protein prra comlexed with2 mg2+
24d1o4ua1
not modelled 95.5 19 Fold:TIM beta/alpha-barrel
Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like
Family:NadC C-terminal domain-like
25c2b7pA_
not modelled 95.5 18 PDB header:transferase
Chain: A: PDB Molecule:probable nicotinate-nucleotide pyrophosphorylase;
PDBTitle: crystal structure of quinolinic acid phosphoribosyltransferase from2 helicobacter pylori
26d1yioa2
not modelled 95.0 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
27d1qpoa1
not modelled 95.0 15 Fold:TIM beta/alpha-barrel
Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like
Family:NadC C-terminal domain-like
28c2jbmA_
not modelled 95.0 19 PDB header:transferase
Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase;
PDBTitle: qprtase structure from human
29c1o4uA_
not modelled 94.9 19 PDB header:transferase
Chain: A: PDB Molecule:type ii quinolic acid phosphoribosyltransferase;
PDBTitle: crystal structure of a nicotinate nucleotide pyrophosphorylase2 (tm1645) from thermotoga maritima at 2.50 a resolution
30d1j5ta_
not modelled 94.6 18 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
31d1wa3a1
not modelled 94.5 21 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
32d1ys7a2
not modelled 94.5 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
33c3qjaA_
not modelled 94.1 14 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of the mycobacterium tuberculosis indole-3-glycerol2 phosphate synthase (trpc) in apo form
34d1mvoa_
not modelled 93.8 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
35d1zesa1
not modelled 93.7 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
36c2c3zA_
not modelled 93.6 19 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of a truncated variant of indole-3-2 glycerol phosphate synthase from sulfolobus solfataricus
37c3hdgE_
not modelled 93.2 16 PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the n-terminal domain of an2 uncharacterized protein (ws1339) from wolinella3 succinogenes
38d1u0sy_
not modelled 93.1 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
39c1qpoA_
not modelled 92.6 17 PDB header:transferase
Chain: A: PDB Molecule:quinolinate acid phosphoribosyl transferase;
PDBTitle: quinolinate phosphoribosyl transferase (qaprtase) apo-enzyme from2 mycobacterium tuberculosis
40d1muma_
not modelled 92.5 14 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like
41d2ayxa1
not modelled 92.5 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
42d1a53a_
not modelled 92.1 19 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
43c3ktoA_
not modelled 92.0 18 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator receiver protein2 from pseudoalteromonas atlantica
44c2yv1A_
not modelled 91.9 27 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
45d1qapa1
not modelled 91.7 19 Fold:TIM beta/alpha-barrel
Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like
Family:NadC C-terminal domain-like
46c3b8iF_
not modelled 91.7 13 PDB header:lyase
Chain: F: PDB Molecule:pa4872 oxaloacetate decarboxylase;
PDBTitle: crystal structure of oxaloacetate decarboxylase from pseudomonas2 aeruginosa (pa4872) in complex with oxalate and mg2+.
47c1x1oC_
not modelled 91.6 16 PDB header:transferase
Chain: C: PDB Molecule:nicotinate-nucleotide pyrophosphorylase;
PDBTitle: crystal structure of project id tt0268 from thermus thermophilus hb8
48c3eooL_
not modelled 91.6 16 PDB header:lyase
Chain: L: PDB Molecule:methylisocitrate lyase;
PDBTitle: 2.9a crystal structure of methyl-isocitrate lyase from2 burkholderia pseudomallei
49c2qr3A_
not modelled 91.4 13 PDB header:transcription
Chain: A: PDB Molecule:two-component system response regulator;
PDBTitle: crystal structure of the n-terminal signal receiver domain of two-2 component system response regulator from bacteroides fragilis
50c3ih1A_
not modelled 91.3 11 PDB header:lyase
Chain: A: PDB Molecule:methylisocitrate lyase;
PDBTitle: crystal structure of carboxyvinyl-carboxyphosphonate phosphorylmutase2 from bacillus anthracis
51d1zh2a1
not modelled 91.2 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
52d1dbwa_
not modelled 91.2 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
53d1peya_
not modelled 90.9 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
54d1i4na_
not modelled 90.8 17 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
55c3jteA_
not modelled 90.5 15 PDB header:protein binding
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator receiver domain2 protein from clostridium thermocellum
56d2nu7b1
not modelled 90.4 15 Fold:Flavodoxin-like
Superfamily:Succinyl-CoA synthetase domains
Family:Succinyl-CoA synthetase domains
57c3tdmD_
not modelled 90.3 9 PDB header:de novo protein
Chain: D: PDB Molecule:computationally designed two-fold symmetric tim-barrel
PDBTitle: computationally designed tim-barrel protein, halfflr
58c2ayxA_
not modelled 90.3 8 PDB header:transferase
Chain: A: PDB Molecule:sensor kinase protein rcsc;
PDBTitle: solution structure of the e.coli rcsc c-terminus (residues2 700-949) containing linker region and phosphoreceiver3 domain
59c1gv1D_
not modelled 90.1 18 PDB header:oxidoreductase
Chain: D: PDB Molecule:malate dehydrogenase;
PDBTitle: structural basis for thermophilic protein stability:2 structures of thermophilic and mesophilic malate3 dehydrogenases
60c1ldbA_
not modelled 89.9 27 PDB header:oxidoreductase(choh(d)-nad(a))
Chain: A: PDB Molecule:apo-l-lactate dehydrogenase;
PDBTitle: structure determination and refinement of bacillus2 stearothermophilus lactate dehydrogenase
61c3eywA_
not modelled 89.8 15 PDB header:transport protein
Chain: A: PDB Molecule:c-terminal domain of glutathione-regulated potassium-efflux
PDBTitle: crystal structure of the c-terminal domain of e. coli kefc in complex2 with keff
62c1ytkA_
not modelled 89.7 23 PDB header:transferase
Chain: A: PDB Molecule:nicotinate phosphoribosyltransferase from thermoplasma
PDBTitle: crystal structure of a nicotinate phosphoribosyltransferase from2 thermoplasma acidophilum with nicotinate mononucleotide
63c3l0gD_
not modelled 89.7 16 PDB header:transferase
Chain: D: PDB Molecule:nicotinate-nucleotide pyrophosphorylase;
PDBTitle: crystal structure of nicotinate-nucleotide pyrophosphorylase from2 ehrlichia chaffeensis at 2.05a resolution
64d1zfja1
not modelled 89.6 16 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
65d2d59a1
not modelled 89.5 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
66c3lyeA_
not modelled 89.3 20 PDB header:hydrolase
Chain: A: PDB Molecule:oxaloacetate acetyl hydrolase;
PDBTitle: crystal structure of oxaloacetate acetylhydrolase
67c2yv2A_
not modelled 89.3 22 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
68c1zlpA_
not modelled 89.1 19 PDB header:lyase
Chain: A: PDB Molecule:petal death protein;
PDBTitle: petal death protein psr132 with cysteine-linked glutaraldehyde forming2 a thiohemiacetal adduct
69d1y81a1
not modelled 89.0 13 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
70c3nhzA_
not modelled 88.3 14 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
71d1y0ea_
not modelled 88.3 19 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:NanE-like
72d1jr1a1
not modelled 88.1 16 Fold:TIM beta/alpha-barrel
Superfamily:Inosine monophosphate dehydrogenase (IMPDH)
Family:Inosine monophosphate dehydrogenase (IMPDH)
73c2jk1A_
not modelled 88.0 16 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
74d1piia2
not modelled 87.9 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
75d1s2wa_
not modelled 87.9 15 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like
76c1me9A_
not modelled 87.8 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine-5'-monophosphate dehydrogenase;
PDBTitle: inosine monophosphate dehydrogenase (impdh) from2 tritrichomonas foetus with imp bound
77c3crnA_
not modelled 87.7 12 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver domain protein, chey-like;
PDBTitle: crystal structure of response regulator receiver domain protein (chey-2 like) from methanospirillum hungatei jf-1
78c1ur5C_
not modelled 87.6 16 PDB header:oxidoreductase
Chain: C: PDB Molecule:malate dehydrogenase;
PDBTitle: stabilization of a tetrameric malate dehydrogenase by2 introduction of a disulfide bridge at the dimer/dimer3 interface
79c3pajA_
not modelled 87.3 19 PDB header:transferase
Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase, carboxylating;
PDBTitle: 2.00 angstrom resolution crystal structure of a quinolinate2 phosphoribosyltransferase from vibrio cholerae o1 biovar eltor str.3 n16961
80c1e8cB_
not modelled 87.2 15 PDB header:ligase
Chain: B: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamate--2,6-
PDBTitle: structure of mure the udp-n-acetylmuramyl tripeptide2 synthetase from e. coli
81d1ny5a1
not modelled 87.1 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
82c1qapA_
not modelled 86.9 19 PDB header:glycosyltransferase
Chain: A: PDB Molecule:quinolinic acid phosphoribosyltransferase;
PDBTitle: quinolinic acid phosphoribosyltransferase with bound2 quinolinic acid
83d1qkka_
not modelled 86.7 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
84d1jbea_
not modelled 86.6 7 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
85c2fpgA_
not modelled 86.5 10 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
86c2jrlA_
not modelled 86.3 10 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: solution structure of the beryllofluoride-activated ntrc4 receiver2 domain dimer
87c2v6bB_
not modelled 86.2 27 PDB header:oxidoreductase
Chain: B: PDB Molecule:l-lactate dehydrogenase;
PDBTitle: crystal structure of lactate dehydrogenase from deinococcus2 radiodurans (apo form)
88c3fa4D_
not modelled 86.1 17 PDB header:lyase
Chain: D: PDB Molecule:2,3-dimethylmalate lyase;
PDBTitle: crystal structure of 2,3-dimethylmalate lyase, a pep mutase/isocitrate2 lyase superfamily member, triclinic crystal form
89d1iuka_
not modelled 86.0 9 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:CoA-binding domain
90d1ujqa_
not modelled 86.0 11 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like
91d1thfd_
not modelled 85.9 8 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
92d1xcfa_
not modelled 85.7 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
93c3dl2A_
not modelled 85.4 24 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:ubiquitin-conjugating enzyme e2 variant 3;
PDBTitle: hexagonal structure of the ldh domain of human ubiquitin-2 conjugating enzyme e2-like isoform a
94c3rqiA_
not modelled 85.3 14 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein;
PDBTitle: crystal structure of a response regulator protein from burkholderia2 pseudomallei with a phosphorylated aspartic acid, calcium ion and3 citrate
95c2v82A_
not modelled 85.3 21 PDB header:lyase
Chain: A: PDB Molecule:2-dehydro-3-deoxy-6-phosphogalactonate aldolase;
PDBTitle: kdpgal complexed to kdpgal
96d2pl1a1
not modelled 84.9 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
97c8ldhA_
not modelled 84.7 20 PDB header:oxidoreductase(choh(d)-nad(a))
Chain: A: PDB Molecule:m4 apo-lactate dehydrogenase;
PDBTitle: refined crystal structure of dogfish m4 apo-lactate2 dehydrogenase
98d1rd5a_
not modelled 84.7 15 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
99c3cu5B_
not modelled 84.7 10 PDB header:transcription regulator
Chain: B: PDB Molecule:two component transcriptional regulator, arac family;
PDBTitle: crystal structure of a two component transcriptional regulator arac2 from clostridium phytofermentans isdg
100c1yadD_
not modelled 84.5 15 PDB header:transcription
Chain: D: PDB Molecule:regulatory protein teni;
PDBTitle: structure of teni from bacillus subtilis
101c2nu8D_
not modelled 84.1 23 PDB header:ligase
Chain: D: PDB Molecule:succinyl-coa ligase [adp-forming] subunit alpha;
PDBTitle: c123at mutant of e. coli succinyl-coa synthetase
102d1vc4a_
not modelled 84.1 22 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
103c2zwmA_
not modelled 83.8 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
104c3a0rB_
not modelled 83.8 8 PDB header:transferase
Chain: B: PDB Molecule:response regulator;
PDBTitle: crystal structure of histidine kinase thka (tm1359) in complex with2 response regulator protein trra (tm1360)
105c2x41A_
not modelled 83.7 23 PDB header:hydrolase
Chain: A: PDB Molecule:beta-glucosidase;
PDBTitle: structure of beta-glucosidase 3b from thermotoga neapolitana2 in complex with glucose
106c2p10D_
not modelled 83.5 21 PDB header:hydrolase
Chain: D: PDB Molecule:mll9387 protein;
PDBTitle: crystal structure of a putative phosphonopyruvate hydrolase (mll9387)2 from mesorhizobium loti maff303099 at 2.15 a resolution
107c2d4aC_
not modelled 83.4 19 PDB header:oxidoreductase
Chain: C: PDB Molecule:malate dehydrogenase;
PDBTitle: structure of the malate dehydrogenase from aeropyrum pernix
108c1hyhA_
not modelled 83.3 27 PDB header:oxidoreductase (choh(d)-nad+(a))
Chain: A: PDB Molecule:l-2-hydroxyisocaproate dehydrogenase;
PDBTitle: crystal structure of l-2-hydroxyisocaproate dehydrogenase from2 lactobacillus confusus at 2.2 angstroms resolution-an example of3 strong asymmetry between subunits
109c3b2nA_
not modelled 83.2 10 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
110c2gjlA_
not modelled 83.1 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:hypothetical protein pa1024;
PDBTitle: crystal structure of 2-nitropropane dioxygenase
111c3tqvA_
not modelled 82.9 16 PDB header:transferase
Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase;
PDBTitle: structure of the nicotinate-nucleotide pyrophosphorylase from2 francisella tularensis.
112c1zn2A_
not modelled 82.9 10 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulatory protein;
PDBTitle: low resolution structure of response regulator styr
113c3cfyA_
not modelled 82.8 8 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative luxo repressor protein;
PDBTitle: crystal structure of signal receiver domain of putative luxo2 repressor protein from vibrio parahaemolyticus
114c3d0oA_
not modelled 82.8 28 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-lactate dehydrogenase 1;
PDBTitle: crystal structure of lactate dehydrogenase from2 staphylococcus aureus
115c3inpA_
not modelled 82.7 14 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.
116d2a9pa1
not modelled 82.6 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
117d1znna1
not modelled 82.5 21 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:PdxS-like
118d1ytda1
not modelled 82.4 23 Fold:TIM beta/alpha-barrel
Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like
Family:NadC C-terminal domain-like
119c3nepX_
not modelled 82.2 16 PDB header:oxidoreductase
Chain: X: PDB Molecule:malate dehydrogenase;
PDBTitle: 1.55a resolution structure of malate dehydrogenase from salinibacter2 ruber
120c3ilmD_
not modelled 82.2 19 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:alr3790 protein;
PDBTitle: crystal structure of the alr3790 protein from anabaena sp. northeast2 structural genomics consortium target nsr437h

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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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