Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP29680
DateThu Jan 5 11:45:39 GMT 2012
Unique Job IDeb23be669b1e582e

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3cyvA_
Top template information
PDB header:lyase
Chain: A: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 shigella flexineri: new insights into its catalytic3 mechanism
Confidence and coverage
Confidence:100.0% Coverage: 99%
352 residues ( 99% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MTELKNDRYLRALLRQPVDVTPVWMMRQAGRYLPEYKATRAQAGDFMSLCKNAELACEVT
Secondary structure 
SS confidence 
Disorder  ?????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LQPLRRYPLDAAILFSDILTVPDAMGLGLYFEAGEGPRFTSPVTCKADVDKLPIPDPEDE
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  LGYVMNAVRTIRRELKGEVPLIGFSGSPWTLATYMVEGGSSKAFTVIKKMMYADPQALHA
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LLDKLAKSVTLYLNAQIKAGAQAVMIFDTWGGVLTGRDYQQFSLYYMHKIVDGLLRENDG
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  RRVPVTLFTKGGGQWLEAMAETGCDALGLDWTTDIADARRRVGNKVALQGNMDPSMLYAP
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350....
Sequence  PARIEEEVATILAGFGHGEGHVFNLGHGIHQDVPPEHAGVFVEAVHRLSEQYHR
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 3cyv chain A

3D model

Region: 3 - 354
Aligned: 352
Modelled: 352
Confidence: 100.0%
Identity: 100%
PDB header:lyase
Chain: A: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 shigella flexineri: new insights into its catalytic3 mechanism

Phyre2

PDB 1r3s chain A

3D model

Region: 2 - 354
Aligned: 351
Modelled: 353
Confidence: 100.0%
Identity: 46%
Fold: TIM beta/alpha-barrel
Superfamily: UROD/MetE-like
Family: Uroporphyrinogen decarboxylase, UROD

Phyre2

PDB 1jpk chain A

3D model

Region: 2 - 354
Aligned: 351
Modelled: 353
Confidence: 100.0%
Identity: 46%
PDB header:lyase
Chain: A: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: gly156asp mutant of human urod, human uroporphyrinogen iii2 decarboxylase

Phyre2

PDB 2inf chain B

3D model

Region: 5 - 351
Aligned: 340
Modelled: 347
Confidence: 100.0%
Identity: 40%
PDB header:lyase
Chain: B: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 bacillus subtilis

Phyre2

PDB 1j93 chain A

3D model

Region: 9 - 349
Aligned: 338
Modelled: 341
Confidence: 100.0%
Identity: 41%
Fold: TIM beta/alpha-barrel
Superfamily: UROD/MetE-like
Family: Uroporphyrinogen decarboxylase, UROD

Phyre2

PDB 2eja chain B

3D model

Region: 5 - 349
Aligned: 334
Modelled: 345
Confidence: 100.0%
Identity: 39%
PDB header:lyase
Chain: B: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 aquifex aeolicus

Phyre2

PDB 3rpd chain B

3D model

Region: 125 - 352
Aligned: 203
Modelled: 213
Confidence: 99.4%
Identity: 10%
PDB header:transferase
Chain: B: PDB Molecule:methionine synthase (b12-independent);
PDBTitle: the structure of a b12-independent methionine synthase from shewanella2 sp. w3-18-1 in complex with selenomethionine.

Phyre2

PDB 1u1h chain A domain 2

3D model

Region: 138 - 351
Aligned: 194
Modelled: 199
Confidence: 99.4%
Identity: 15%
Fold: TIM beta/alpha-barrel
Superfamily: UROD/MetE-like
Family: Cobalamin-independent methionine synthase

Phyre2

PDB 1u22 chain A

3D model

Region: 138 - 348
Aligned: 194
Modelled: 196
Confidence: 99.3%
Identity: 15%
PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--
PDBTitle: a. thaliana cobalamine independent methionine synthase

Phyre2

PDB 1t7l chain A

3D model

Region: 125 - 353
Aligned: 206
Modelled: 209
Confidence: 99.3%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--
PDBTitle: crystal structure of cobalamin-independent methionine2 synthase from t. maritima

Phyre2

PDB 2nq5 chain A

3D model

Region: 125 - 351
Aligned: 193
Modelled: 197
Confidence: 99.2%
Identity: 12%
PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--
PDBTitle: crystal structure of methyltransferase from streptococcus2 mutans

Phyre2

PDB 3l7s chain A

3D model

Region: 125 - 352
Aligned: 209
Modelled: 213
Confidence: 99.2%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--homocysteine
PDBTitle: crystal structure of mete coordinated with zinc from streptococcus2 mutans

Phyre2

PDB 1ypx chain A

3D model

Region: 124 - 348
Aligned: 208
Modelled: 225
Confidence: 99.2%
Identity: 11%
PDB header:transferase
Chain: A: PDB Molecule:putative vitamin-b12 independent methionine synthase family
PDBTitle: crystal structure of the putative vitamin-b12 independent methionine2 synthase from listeria monocytogenes, northeast structural genomics3 target lmr13

Phyre2

PDB 1u1h chain A domain 1

3D model

Region: 126 - 330
Aligned: 188
Modelled: 205
Confidence: 98.4%
Identity: 15%
Fold: TIM beta/alpha-barrel
Superfamily: UROD/MetE-like
Family: Cobalamin-independent methionine synthase

Phyre2

PDB 1tx2 chain A

3D model

Region: 186 - 341
Aligned: 147
Modelled: 155
Confidence: 96.1%
Identity: 12%
Fold: TIM beta/alpha-barrel
Superfamily: Dihydropteroate synthetase-like
Family: Dihydropteroate synthetase

Phyre2

PDB 1tx2 chain A

3D model

Region: 186 - 341
Aligned: 147
Modelled: 155
Confidence: 96.1%
Identity: 12%
PDB header:transferase
Chain: A: PDB Molecule:dhps, dihydropteroate synthase;
PDBTitle: dihydropteroate synthetase, with bound inhibitor manic, from bacillus2 anthracis

Phyre2

PDB 1pii chain A

3D model

Region: 58 - 348
Aligned: 261
Modelled: 266
Confidence: 95.7%
Identity: 18%
PDB header:bifunctional(isomerase and synthase)
Chain: A: PDB Molecule:n-(5'phosphoribosyl)anthranilate isomerase;
PDBTitle: three-dimensional structure of the bifunctional enzyme2 phosphoribosylanthranilate isomerase:3 indoleglycerolphosphate synthase from escherichia coli4 refined at 2.0 angstroms resolution

Phyre2

PDB 3lci chain A

3D model

Region: 187 - 343
Aligned: 131
Modelled: 142
Confidence: 95.7%
Identity: 12%
PDB header:lyase
Chain: A: PDB Molecule:n-acetylneuraminate lyase;
PDBTitle: the d-sialic acid aldolase mutant v251w

Phyre2

PDB 3bg3 chain B

3D model

Region: 187 - 269
Aligned: 71
Modelled: 83
Confidence: 95.2%
Identity: 20%
PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase, mitochondrial;
PDBTitle: crystal structure of human pyruvate carboxylase (missing2 the biotin carboxylase domain at the n-terminus)

Phyre2

PDB 3bi8 chain A

3D model

Region: 187 - 343
Aligned: 125
Modelled: 135
Confidence: 95.0%
Identity: 16%
PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: structure of dihydrodipicolinate synthase from clostridium2 botulinum

Phyre2
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c3cyvA_
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d1r3sa_
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c1jpkA_
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c2infB_
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d1j93a_
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c2ejaB_
7
c3rpdB_
8
d1u1ha2
9
c1u22A_
10
c1t7lA_
11
c2nq5A_
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c3l7sA_
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c1ypxA_
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d1u1ha1
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d1tx2a_
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c1tx2A_
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c1piiA_
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c3lciA_
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c3bg3B_
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c3bi8A_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3cyvA_
100.0 100 PDB header:lyase
Chain: A: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 shigella flexineri: new insights into its catalytic3 mechanism
2d1r3sa_
100.0 46 Fold:TIM beta/alpha-barrel
Superfamily:UROD/MetE-like
Family:Uroporphyrinogen decarboxylase, UROD
3c1jpkA_
100.0 46 PDB header:lyase
Chain: A: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: gly156asp mutant of human urod, human uroporphyrinogen iii2 decarboxylase
4c2infB_
100.0 40 PDB header:lyase
Chain: B: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 bacillus subtilis
5d1j93a_
100.0 41 Fold:TIM beta/alpha-barrel
Superfamily:UROD/MetE-like
Family:Uroporphyrinogen decarboxylase, UROD
6c2ejaB_
100.0 39 PDB header:lyase
Chain: B: PDB Molecule:uroporphyrinogen decarboxylase;
PDBTitle: crystal structure of uroporphyrinogen decarboxylase from2 aquifex aeolicus
7c3rpdB_
99.4 10 PDB header:transferase
Chain: B: PDB Molecule:methionine synthase (b12-independent);
PDBTitle: the structure of a b12-independent methionine synthase from shewanella2 sp. w3-18-1 in complex with selenomethionine.
8d1u1ha2
99.4 15 Fold:TIM beta/alpha-barrel
Superfamily:UROD/MetE-like
Family:Cobalamin-independent methionine synthase
9c1u22A_
99.3 15 PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--
PDBTitle: a. thaliana cobalamine independent methionine synthase
10c1t7lA_
99.3 14 PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--
PDBTitle: crystal structure of cobalamin-independent methionine2 synthase from t. maritima
11c2nq5A_
99.2 12 PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--
PDBTitle: crystal structure of methyltransferase from streptococcus2 mutans
12c3l7sA_
99.2 13 PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--homocysteine
PDBTitle: crystal structure of mete coordinated with zinc from streptococcus2 mutans
13c1ypxA_
99.2 11 PDB header:transferase
Chain: A: PDB Molecule:putative vitamin-b12 independent methionine synthase family
PDBTitle: crystal structure of the putative vitamin-b12 independent methionine2 synthase from listeria monocytogenes, northeast structural genomics3 target lmr13
14d1u1ha1
98.4 15 Fold:TIM beta/alpha-barrel
Superfamily:UROD/MetE-like
Family:Cobalamin-independent methionine synthase
15d1tx2a_
96.1 12 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
16c1tx2A_
96.1 12 PDB header:transferase
Chain: A: PDB Molecule:dhps, dihydropteroate synthase;
PDBTitle: dihydropteroate synthetase, with bound inhibitor manic, from bacillus2 anthracis
17c1piiA_
95.7 18 PDB header:bifunctional(isomerase and synthase)
Chain: A: PDB Molecule:n-(5'phosphoribosyl)anthranilate isomerase;
PDBTitle: three-dimensional structure of the bifunctional enzyme2 phosphoribosylanthranilate isomerase:3 indoleglycerolphosphate synthase from escherichia coli4 refined at 2.0 angstroms resolution
18c3lciA_
95.7 12 PDB header:lyase
Chain: A: PDB Molecule:n-acetylneuraminate lyase;
PDBTitle: the d-sialic acid aldolase mutant v251w
19c3bg3B_
95.2 20 PDB header:ligase
Chain: B: PDB Molecule:pyruvate carboxylase, mitochondrial;
PDBTitle: crystal structure of human pyruvate carboxylase (missing2 the biotin carboxylase domain at the n-terminus)
20c3bi8A_
95.0 16 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: structure of dihydrodipicolinate synthase from clostridium2 botulinum
21c3d0cB_
not modelled 94.9 15 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 oceanobacillus iheyensis at 1.9 a resolution
22c3daqB_
not modelled 94.8 19 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from methicillin-2 resistant staphylococcus aureus
23d1qopa_
not modelled 94.8 15 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
24c3n2xB_
not modelled 94.8 19 PDB header:lyase
Chain: B: PDB Molecule:uncharacterized protein yage;
PDBTitle: crystal structure of yage, a prophage protein belonging to the2 dihydrodipicolinic acid synthase family from e. coli k12 in complex3 with pyruvate
25c3h5dD_
not modelled 94.5 13 PDB header:lyase
Chain: D: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: dihydrodipicolinate synthase from drug-resistant streptococcus2 pneumoniae
26c3qfwB_
not modelled 94.5 17 PDB header:lyase
Chain: B: PDB Molecule:ribulose-1,5-bisphosphate carboxylase/oxygenase large
PDBTitle: crystal structure of rubisco-like protein from rhodopseudomonas2 palustris
27d1xkya1
not modelled 94.5 16 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
28c2v9dB_
not modelled 94.4 19 PDB header:lyase
Chain: B: PDB Molecule:yage;
PDBTitle: crystal structure of yage, a prophage protein belonging to2 the dihydrodipicolinic acid synthase family from e. coli3 k12
29c3noeA_
not modelled 94.2 18 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from pseudomonas2 aeruginosa
30d1ad1a_
not modelled 93.9 14 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
31c2ehhE_
not modelled 93.7 16 PDB header:lyase
Chain: E: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 aquifex aeolicus
32c3pueA_
not modelled 93.5 20 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of the complex of dhydrodipicolinate synthase from2 acinetobacter baumannii with lysine at 2.6a resolution
33c2h9aB_
not modelled 93.4 12 PDB header:oxidoreductase
Chain: B: PDB Molecule:co dehydrogenase/acetyl-coa synthase, iron-
PDBTitle: corrinoid iron-sulfur protein
34c2y5sA_
not modelled 93.4 14 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase;
PDBTitle: crystal structure of burkholderia cenocepacia dihydropteroate2 synthase complexed with 7,8-dihydropteroate.
35c2r8wB_
not modelled 93.3 13 PDB header:lyase
Chain: B: PDB Molecule:agr_c_1641p;
PDBTitle: the crystal structure of dihydrodipicolinate synthase (atu0899) from2 agrobacterium tumefaciens str. c58
36c2bmbA_
not modelled 93.2 12 PDB header:transferase
Chain: A: PDB Molecule:folic acid synthesis protein fol1;
PDBTitle: x-ray structure of the bifunctional 6-hydroxymethyl-7,8-2 dihydroxypterin pyrophosphokinase dihydropteroate synthase3 from saccharomyces cerevisiae
37c3lerA_
not modelled 93.2 15 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 campylobacter jejuni subsp. jejuni nctc 11168
38d1hl2a_
not modelled 93.2 15 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
39c3bg5C_
not modelled 93.1 15 PDB header:ligase
Chain: C: PDB Molecule:pyruvate carboxylase;
PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase
40c2rfgB_
not modelled 93.1 19 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from hahella2 chejuensis at 1.5a resolution
41d1d9ea_
not modelled 92.9 14 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I DAHP synthetase
42d1vlia2
not modelled 92.9 15 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:NeuB-like
43c2h90A_
not modelled 92.4 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:xenobiotic reductase a;
PDBTitle: xenobiotic reductase a in complex with coumarin
44d1o5ka_
not modelled 91.7 15 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
45d2a6na1
not modelled 91.6 17 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
46c2vc6A_
not modelled 91.5 18 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: structure of mosa from s. meliloti with pyruvate bound
47c3eb2A_
not modelled 91.5 13 PDB header:lyase
Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 rhodopseudomonas palustris at 2.0a resolution
48c2qygC_
not modelled 91.5 13 PDB header:unknown function
Chain: C: PDB Molecule:ribulose bisphosphate carboxylase-like protein 2;
PDBTitle: crystal structure of a rubisco-like protein rlp2 from rhodopseudomonas2 palustris
49d1xxxa1
not modelled 91.3 14 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
50c1rr2A_
not modelled 91.2 12 PDB header:transferase
Chain: A: PDB Molecule:transcarboxylase 5s subunit;
PDBTitle: propionibacterium shermanii transcarboxylase 5s subunit bound to 2-2 ketobutyric acid
51c3f4wA_
not modelled 91.2 15 PDB header:synthase, lyase
Chain: A: PDB Molecule:putative hexulose 6 phosphate synthase;
PDBTitle: the 1.65a crystal structure of 3-hexulose-6-phosphate2 synthase from salmonella typhimurium
52c3g0sA_
not modelled 91.0 18 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: dihydrodipicolinate synthase from salmonella typhimurium lt2
53c3gr7A_
not modelled 90.8 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadph dehydrogenase;
PDBTitle: structure of oye from geobacillus kaustophilus, hexagonal2 crystal form
54d1ps9a1
not modelled 90.6 12 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
55c2d69B_
not modelled 90.2 15 PDB header:lyase
Chain: B: PDB Molecule:ribulose bisphosphate carboxylase;
PDBTitle: crystal structure of the complex of sulfate ion and octameric2 ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from3 pyrococcus horikoshii ot3 (form-2 crystal)
56c3stgA_
not modelled 90.2 18 PDB header:transferase
Chain: A: PDB Molecule:2-dehydro-3-deoxyphosphooctonate aldolase;
PDBTitle: crystal structure of a58p, del(n59), and loop 7 truncated mutant of 3-2 deoxy-d-manno-octulosonate 8-phosphate synthase (kdo8ps) from3 neisseria meningitidis
57c3fluD_
not modelled 90.1 18 PDB header:lyase
Chain: D: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from the pathogen2 neisseria meningitidis
58c3cprB_
not modelled 90.1 14 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthetase;
PDBTitle: the crystal structure of corynebacterium glutamicum2 dihydrodipicolinate synthase to 2.2 a resolution
59d1ajza_
not modelled 90.0 14 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
60c3sz8D_
not modelled 90.0 16 PDB header:transferase
Chain: D: PDB Molecule:2-dehydro-3-deoxyphosphooctonate aldolase 2;
PDBTitle: crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from2 burkholderia pseudomallei
61c2vefB_
not modelled 89.8 17 PDB header:transferase
Chain: B: PDB Molecule:dihydropteroate synthase;
PDBTitle: dihydropteroate synthase from streptococcus pneumoniae
62c3s5oA_
not modelled 89.7 11 PDB header:lyase
Chain: A: PDB Molecule:4-hydroxy-2-oxoglutarate aldolase, mitochondrial;
PDBTitle: crystal structure of human 4-hydroxy-2-oxoglutarate aldolase bound to2 pyruvate
63d1piia1
not modelled 89.7 18 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
64d2d69a1
not modelled 89.7 15 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
65c3na8A_
not modelled 89.2 15 PDB header:lyase
Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase;
PDBTitle: crystal structure of a putative dihydrodipicolinate synthetase from2 pseudomonas aeruginosa
66c3dz1A_
not modelled 89.1 14 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 rhodopseudomonas palustris at 1.87a resolution
67c1telA_
not modelled 89.0 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:ribulose bisphosphate carboxylase, large subunit;
PDBTitle: crystal structure of a rubisco-like protein from chlorobium2 tepidum
68c2nx9B_
not modelled 88.5 16 PDB header:lyase
Chain: B: PDB Molecule:oxaloacetate decarboxylase 2, subunit alpha;
PDBTitle: crystal structure of the carboxyltransferase domain of the2 oxaloacetate decarboxylase na+ pump from vibrio cholerae
69c3si9B_
not modelled 88.5 15 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from bartonella2 henselae
70c3e96B_
not modelled 88.4 13 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 bacillus clausii
71d1r74a_
not modelled 88.3 19 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Glycine N-methyltransferase
72c2vp8A_
not modelled 88.3 11 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase 2;
PDBTitle: structure of mycobacterium tuberculosis rv1207
73c2yxgD_
not modelled 88.2 14 PDB header:lyase
Chain: D: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihyrodipicolinate synthase (dapa)
74d1q6oa_
not modelled 87.0 17 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Decarboxylase
75c1x7fA_
not modelled 86.9 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:outer surface protein;
PDBTitle: crystal structure of an uncharacterized b. cereus protein
76d1o60a_
not modelled 86.9 14 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I DAHP synthetase
77c3bolB_
not modelled 86.4 17 PDB header:transferase
Chain: B: PDB Molecule:5-methyltetrahydrofolate s-homocysteine
PDBTitle: cobalamin-dependent methionine synthase (1-566) from2 thermotoga maritima complexed with zn2+
78d1xvaa_
not modelled 85.8 22 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Glycine N-methyltransferase
79c1zcoA_
not modelled 85.7 13 PDB header:lyase
Chain: A: PDB Molecule:2-dehydro-3-deoxyphosphoheptonate aldolase;
PDBTitle: crystal structure of pyrococcus furiosus 3-deoxy-d-arabino-2 heptulosonate 7-phosphate synthase
80d1eyea_
not modelled 85.6 15 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
81d1f74a_
not modelled 85.6 16 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
82c2yciX_
not modelled 85.5 12 PDB header:transferase
Chain: X: PDB Molecule:5-methyltetrahydrofolate corrinoid/iron sulfur protein
PDBTitle: methyltransferase native
83c1nvmG_
not modelled 85.3 13 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
84c3mcnA_
not modelled 85.2 14 PDB header:transferase
Chain: A: PDB Molecule:2-amino-4-hydroxy-6-hydroxymethyldihydropteridine
PDBTitle: crystal structure of the 6-hyroxymethyl-7,8-dihydropterin2 pyrophosphokinase dihydropteroate synthase bifunctional enzyme from3 francisella tularensis
85d1x7fa2
not modelled 84.5 22 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Outer surface protein, N-terminal domain
86c3hf3A_
not modelled 83.6 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:chromate reductase;
PDBTitle: old yellow enzyme from thermus scotoductus sa-01
87c2ze3A_
not modelled 83.0 23 PDB header:isomerase
Chain: A: PDB Molecule:dfa0005;
PDBTitle: crystal structure of dfa0005 complexed with alpha-ketoglutarate: a2 novel member of the icl/pepm superfamily from alkali-tolerant3 deinococcus ficus
88c1xuzA_
not modelled 82.9 15 PDB header:biosynthetic protein
Chain: A: PDB Molecule:polysialic acid capsule biosynthesis protein siac;
PDBTitle: crystal structure analysis of sialic acid synthase (neub)from2 neisseria meningitidis, bound to mn2+, phosphoenolpyruvate, and n-3 acetyl mannosaminitol
89c3gkaB_
not modelled 82.9 18 PDB header:oxidoreductase
Chain: B: PDB Molecule:n-ethylmaleimide reductase;
PDBTitle: crystal structure of n-ethylmaleimidine reductase from2 burkholderia pseudomallei
90c3q94B_
not modelled 82.7 20 PDB header:lyase
Chain: B: PDB Molecule:fructose-bisphosphate aldolase, class ii;
PDBTitle: the crystal structure of fructose 1,6-bisphosphate aldolase from2 bacillus anthracis str. 'ames ancestor'
91c3qfeB_
not modelled 82.5 13 PDB header:lyase
Chain: B: PDB Molecule:putative dihydrodipicolinate synthase family protein;
PDBTitle: crystal structures of a putative dihydrodipicolinate synthase family2 protein from coccidioides immitis
92c3gndC_
not modelled 82.1 16 PDB header:lyase
Chain: C: PDB Molecule:aldolase lsrf;
PDBTitle: crystal structure of e. coli lsrf in complex with ribulose-5-phosphate
93c3b4uB_
not modelled 81.7 14 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from agrobacterium2 tumefaciens str. c58
94d1ccwa_
not modelled 81.2 18 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
95c2r94B_
not modelled 81.2 14 PDB header:lyase
Chain: B: PDB Molecule:2-keto-3-deoxy-(6-phospho-)gluconate aldolase;
PDBTitle: crystal structure of kd(p)ga from t.tenax
96d1vjia_
not modelled 81.0 17 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
97c3t4cD_
not modelled 80.8 13 PDB header:transferase
Chain: D: PDB Molecule:2-dehydro-3-deoxyphosphooctonate aldolase 1;
PDBTitle: crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from2 burkholderia ambifaria
98c3bleA_
not modelled 80.4 15 PDB header:transferase
Chain: A: PDB Molecule:citramalate synthase from leptospira interrogans;
PDBTitle: crystal structure of the catalytic domain of licms in2 complexed with malonate
99c3fkkA_
not modelled 80.2 18 PDB header:lyase
Chain: A: PDB Molecule:l-2-keto-3-deoxyarabonate dehydratase;
PDBTitle: structure of l-2-keto-3-deoxyarabonate dehydratase
100d1nvma2
not modelled 80.1 11 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:HMGL-like
101d3bofa1
not modelled 79.9 14 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Methyltetrahydrofolate-utiluzing methyltransferases
102d1rbla1
not modelled 79.9 14 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
103d1olta_
not modelled 79.6 10 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:Oxygen-independent coproporphyrinogen III oxidase HemN
104c3igsB_
not modelled 78.6 18 PDB header:isomerase
Chain: B: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase 2;
PDBTitle: structure of the salmonella enterica n-acetylmannosamine-6-phosphate2 2-epimerase
105d1w3ia_
not modelled 78.1 8 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
106d2zdra2
not modelled 78.1 15 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:NeuB-like
107d3bofa2
not modelled 78.1 13 Fold:TIM beta/alpha-barrel
Superfamily:Homocysteine S-methyltransferase
Family:Homocysteine S-methyltransferase
108d1f6ya_
not modelled 77.9 9 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Methyltetrahydrofolate-utiluzing methyltransferases
109d1rvga_
not modelled 77.4 14 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class II FBP aldolase
110d1icpa_
not modelled 76.9 18 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
111d1gvfa_
not modelled 76.8 13 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class II FBP aldolase
112d7reqa2
not modelled 76.5 15 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
113c2hmcA_
not modelled 76.2 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: the crystal structure of dihydrodipicolinate synthase dapa from2 agrobacterium tumefaciens
114c3b8iF_
not modelled 76.2 21 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+.
115c3tr9A_
not modelled 75.9 11 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase;
PDBTitle: structure of a dihydropteroate synthase (folp) in complex with pteroic2 acid from coxiella burnetii
116c1vliA_
not modelled 75.8 13 PDB header:biosynthetic protein
Chain: A: PDB Molecule:spore coat polysaccharide biosynthesis protein spse;
PDBTitle: crystal structure of spore coat polysaccharide biosynthesis protein2 spse (bsu37870) from bacillus subtilis at 2.38 a resolution
117c3f4cA_
not modelled 75.1 12 PDB header:hydrolase
Chain: A: PDB Molecule:organophosphorus hydrolase;
PDBTitle: crystal structure of organophosphorus hydrolase from geobacillus2 stearothermophilus strain 10, with glycerol bound
118d1gwja_
not modelled 75.1 19 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
119d1xrsb1
not modelled 73.8 18 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
120c2nuxB_
not modelled 73.0 11 PDB header:lyase
Chain: B: PDB Molecule:2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate
PDBTitle: 2-keto-3-deoxygluconate aldolase from sulfolobus acidocaldarius,2 native structure in p6522 at 2.5 a resolution

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