Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP13009
DateThu Jan 5 11:33:23 GMT 2012
Unique Job ID040ac6e1ba337e6a

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1k98A_
Top template information
PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment
Confidence and coverage
Confidence:100.0% Coverage: 47%
577 residues ( 47% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
1126 residues ( 92%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK
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Disorder  ?????




























?????



?
??
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   .........70.........80.........90.........100.........110.........120
Sequence  PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA
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?????






















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   .........130.........140.........150.........160.........170.........180
Sequence  RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI
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Disorder  ??


















?

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   .........190.........200.........210.........220.........230.........240
Sequence  ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA
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   .........250.........260.........270.........280.........290.........300
Sequence  LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ
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   .........310.........320.........330.........340.........350.........360
Sequence  AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG
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?????????













?
?
??
??
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   .........370.........380.........390.........400.........410.........420
Sequence  ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI
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   .........430.........440.........450.........460.........470.........480
Sequence  AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV
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??
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   .........490.........500.........510.........520.........530.........540
Sequence  VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ
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?
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   .........550.........560.........570.........580.........590.........600
Sequence  DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG
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   .........610.........620.........630.........640.........650.........660
Sequence  QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN
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   .........670.........680.........690.........700.........710.........720
Sequence  KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK
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   .........730.........740.........750.........760.........770.........780
Sequence  SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL
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   .........790.........800.........810.........820.........830.........840
Sequence  GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA
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   .........850.........860.........870.........880.........890.........900
Sequence  HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR
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???????
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   .........910.........920.........930.........940.........950.........960
Sequence  TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEASIETLRNYIDWTPFFMTWSLAGKY
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Disorder  ?????????????


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??????
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   .........970.........980.........990.........1000.........1010.........1020
Sequence  PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT
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Disorder  ??

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   .........1030.........1040.........1050.........1060.........1070.........1080
Sequence  HVINVSHHLRQQTEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQH
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?????????









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???
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   .........1090.........1100.........1110.........1120.........1130.........1140
Sequence  DDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYP
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   .........1150.........1160.........1170.........1180.........1190.........1200
Sequence  ACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQV
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   .........1210.........1220.......
Sequence  EDYARRKGMSVTEVERWLAPNLGYDAD
Secondary structure 









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Disorder 





??












??????
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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 1k98 chain A

3D model

Region: 651 - 1227
Aligned: 577
Modelled: 577
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment

Phyre2

PDB 3bol chain B

3D model

Region: 2 - 620
Aligned: 549
Modelled: 595
Confidence: 100.0%
Identity: 29%
PDB header:transferase
Chain: B: PDB Molecule:5-methyltetrahydrofolate s-homocysteine
PDBTitle: cobalamin-dependent methionine synthase (1-566) from2 thermotoga maritima complexed with zn2+

Phyre2

PDB 1msk chain A

3D model

Region: 901 - 1227
Aligned: 327
Modelled: 327
Confidence: 100.0%
Identity: 100%
Fold: Methionine synthase activation domain-like
Superfamily: Methionine synthase activation domain-like
Family: Methionine synthase SAM-binding domain

Phyre2

PDB 2o2k chain A

3D model

Region: 900 - 1225
Aligned: 325
Modelled: 326
Confidence: 100.0%
Identity: 49%
PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: crystal structure of the activation domain of human2 methionine synthase isoform/mutant d963e/k1071n

Phyre2

PDB 1umy chain A

3D model

Region: 8 - 393
Aligned: 334
Modelled: 371
Confidence: 100.0%
Identity: 23%
Fold: TIM beta/alpha-barrel
Superfamily: Homocysteine S-methyltransferase
Family: Homocysteine S-methyltransferase

Phyre2

PDB 3k13 chain A

3D model

Region: 353 - 639
Aligned: 286
Modelled: 287
Confidence: 100.0%
Identity: 64%
PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydrofolate-homocysteine methyltransferase;
PDBTitle: structure of the pterin-binding domain metr of 5-2 methyltetrahydrofolate-homocysteine methyltransferase from3 bacteroides thetaiotaomicron

Phyre2

PDB 3bof chain A domain 2

3D model

Region: 2 - 337
Aligned: 296
Modelled: 319
Confidence: 100.0%
Identity: 33%
Fold: TIM beta/alpha-barrel
Superfamily: Homocysteine S-methyltransferase
Family: Homocysteine S-methyltransferase

Phyre2

PDB 1lt7 chain A

3D model

Region: 6 - 369
Aligned: 282
Modelled: 318
Confidence: 100.0%
Identity: 25%
Fold: TIM beta/alpha-barrel
Superfamily: Homocysteine S-methyltransferase
Family: Homocysteine S-methyltransferase

Phyre2

PDB 2yci chain X

3D model

Region: 351 - 637
Aligned: 266
Modelled: 287
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: X: PDB Molecule:5-methyltetrahydrofolate corrinoid/iron sulfur protein
PDBTitle: methyltransferase native

Phyre2

PDB 3bof chain A domain 1

3D model

Region: 340 - 620
Aligned: 259
Modelled: 280
Confidence: 100.0%
Identity: 24%
Fold: TIM beta/alpha-barrel
Superfamily: Dihydropteroate synthetase-like
Family: Methyltetrahydrofolate-utiluzing methyltransferases

Phyre2

PDB 1bmt chain B

3D model

Region: 651 - 896
Aligned: 246
Modelled: 246
Confidence: 100.0%
Identity: 100%
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 1f6y chain A

3D model

Region: 356 - 637
Aligned: 257
Modelled: 282
Confidence: 100.0%
Identity: 26%
Fold: TIM beta/alpha-barrel
Superfamily: Dihydropteroate synthetase-like
Family: Methyltetrahydrofolate-utiluzing methyltransferases

Phyre2

PDB 2i2x chain D

3D model

Region: 661 - 887
Aligned: 215
Modelled: 227
Confidence: 100.0%
Identity: 32%
PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri

Phyre2

PDB 3ezx chain A

3D model

Region: 655 - 871
Aligned: 208
Modelled: 217
Confidence: 100.0%
Identity: 26%
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: 741 - 896
Aligned: 156
Modelled: 156
Confidence: 100.0%
Identity: 99%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1xrs chain B

3D model

Region: 668 - 871
Aligned: 181
Modelled: 201
Confidence: 100.0%
Identity: 19%
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 1tx2 chain A

3D model

Region: 345 - 598
Aligned: 234
Modelled: 254
Confidence: 100.0%
Identity: 21%
PDB header:transferase
Chain: A: PDB Molecule:dhps, dihydropteroate synthase;
PDBTitle: dihydropteroate synthetase, with bound inhibitor manic, from bacillus2 anthracis

Phyre2

PDB 1tx2 chain A

3D model

Region: 345 - 598
Aligned: 234
Modelled: 254
Confidence: 100.0%
Identity: 21%
Fold: TIM beta/alpha-barrel
Superfamily: Dihydropteroate synthetase-like
Family: Dihydropteroate synthetase

Phyre2

PDB 1j6r chain A

3D model

Region: 945 - 1181
Aligned: 180
Modelled: 222
Confidence: 100.0%
Identity: 17%
Fold: Methionine synthase activation domain-like
Superfamily: Methionine synthase activation domain-like
Family: Hypothetical protein TM0269

Phyre2

PDB 1ad1 chain A

3D model

Region: 354 - 598
Aligned: 229
Modelled: 245
Confidence: 100.0%
Identity: 20%
Fold: TIM beta/alpha-barrel
Superfamily: Dihydropteroate synthetase-like
Family: Dihydropteroate synthetase

Phyre2
1

c1k98A_
2

c3bolB_
3

d1mska_
4

c2o2kA_
5

d1umya_
6

c3k13A_
7

d3bofa2
8

d1lt7a_
9

c2yciX_
10

d3bofa1
11

c1bmtB_
12

d1f6ya_
13

c2i2xD_
14

c3ezxA_
15

d3bula2
16

c1xrsB_
17

c1tx2A_
18

d1tx2a_
19

d1j6ra_
20

d1ad1a_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1k98A_



100.0 100 PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment
2c3bolB_



100.0 29 PDB header:transferase
Chain: B: PDB Molecule:5-methyltetrahydrofolate s-homocysteine
PDBTitle: cobalamin-dependent methionine synthase (1-566) from2 thermotoga maritima complexed with zn2+
3d1mska_



100.0 100 Fold:Methionine synthase activation domain-like
Superfamily:Methionine synthase activation domain-like
Family:Methionine synthase SAM-binding domain
4c2o2kA_



100.0 49 PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: crystal structure of the activation domain of human2 methionine synthase isoform/mutant d963e/k1071n
5d1umya_



100.0 23 Fold:TIM beta/alpha-barrel
Superfamily:Homocysteine S-methyltransferase
Family:Homocysteine S-methyltransferase
6c3k13A_



100.0 64 PDB header:transferase
Chain: A: PDB Molecule:5-methyltetrahydrofolate-homocysteine methyltransferase;
PDBTitle: structure of the pterin-binding domain metr of 5-2 methyltetrahydrofolate-homocysteine methyltransferase from3 bacteroides thetaiotaomicron
7d3bofa2



100.0 33 Fold:TIM beta/alpha-barrel
Superfamily:Homocysteine S-methyltransferase
Family:Homocysteine S-methyltransferase
8d1lt7a_



100.0 25 Fold:TIM beta/alpha-barrel
Superfamily:Homocysteine S-methyltransferase
Family:Homocysteine S-methyltransferase
9c2yciX_



100.0 25 PDB header:transferase
Chain: X: PDB Molecule:5-methyltetrahydrofolate corrinoid/iron sulfur protein
PDBTitle: methyltransferase native
10d3bofa1



100.0 24 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Methyltetrahydrofolate-utiluzing methyltransferases
11c1bmtB_



100.0 100 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
12d1f6ya_



100.0 26 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Methyltetrahydrofolate-utiluzing methyltransferases
13c2i2xD_



100.0 32 PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri
14c3ezxA_



100.0 26 PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein
15d3bula2



100.0 99 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
16c1xrsB_



100.0 19 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
17c1tx2A_



100.0 21 PDB header:transferase
Chain: A: PDB Molecule:dhps, dihydropteroate synthase;
PDBTitle: dihydropteroate synthetase, with bound inhibitor manic, from bacillus2 anthracis
18d1tx2a_



100.0 21 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
19d1j6ra_



100.0 17 Fold:Methionine synthase activation domain-like
Superfamily:Methionine synthase activation domain-like
Family:Hypothetical protein TM0269
20d1ad1a_



100.0 20 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
21d1ajza_



not modelled 100.0 21 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
22c2y5sA_



not modelled 99.9 19 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase;
PDBTitle: crystal structure of burkholderia cenocepacia dihydropteroate2 synthase complexed with 7,8-dihydropteroate.
23d1xrsb1



not modelled 99.9 19 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
24c3tr9A_



not modelled 99.9 17 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase;
PDBTitle: structure of a dihydropteroate synthase (folp) in complex with pteroic2 acid from coxiella burnetii
25c2vp8A_



not modelled 99.9 15 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase 2;
PDBTitle: structure of mycobacterium tuberculosis rv1207
26d1eyea_



not modelled 99.9 19 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
27c2dzaA_



not modelled 99.9 23 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase;
PDBTitle: crystal structure of dihydropteroate synthase from thermus2 thermophilus hb8 in complex with 4-aminobenzoate
28c1y80A_



not modelled 99.9 30 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
29d3bula1



not modelled 99.9 99 Fold:Methionine synthase domain-like
Superfamily:Methionine synthase domain
Family:Methionine synthase domain
30c2h9aB_



not modelled 99.9 17 PDB header:oxidoreductase
Chain: B: PDB Molecule:co dehydrogenase/acetyl-coa synthase, iron-
PDBTitle: corrinoid iron-sulfur protein
31c2vefB_



not modelled 99.8 27 PDB header:transferase
Chain: B: PDB Molecule:dihydropteroate synthase;
PDBTitle: dihydropteroate synthase from streptococcus pneumoniae
32d7reqa2



not modelled 99.8 16 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
33d1ccwa_



not modelled 99.8 22 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
34d1fmfa_



not modelled 99.7 20 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
35c2yxbA_



not modelled 99.6 18 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
36c2h9aA_



not modelled 99.4 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:carbon monoxide dehydrogenase corrinoid/iron-
PDBTitle: corrinoid iron-sulfur protein
37c3mcnA_



not modelled 99.3 19 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
38c2bmbA_



not modelled 99.3 19 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
39c3bicA_



not modelled 99.1 13 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase, mitochondrial precursor;
PDBTitle: crystal structure of human methylmalonyl-coa mutase
40c3noyA_



not modelled 99.0 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase;
PDBTitle: crystal structure of ispg (gcpe)
41c3koxA_



not modelled 98.4 29 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)
42c1e1cA_



not modelled 97.8 17 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant
43d1ka9f_



not modelled 97.4 19 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
44d1xxxa1



not modelled 96.4 16 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
45c2v9dB_



not modelled 96.4 14 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
46c3s5oA_



not modelled 96.3 15 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
47c3n2xB_



not modelled 96.2 15 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
48c2ehhE_



not modelled 96.1 13 PDB header:lyase
Chain: E: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 aquifex aeolicus
49c3fkkA_



not modelled 96.0 13 PDB header:lyase
Chain: A: PDB Molecule:l-2-keto-3-deoxyarabonate dehydratase;
PDBTitle: structure of l-2-keto-3-deoxyarabonate dehydratase
50c2r8wB_



not modelled 95.9 12 PDB header:lyase
Chain: B: PDB Molecule:agr_c_1641p;
PDBTitle: the crystal structure of dihydrodipicolinate synthase (atu0899) from2 agrobacterium tumefaciens str. c58
51c3si9B_



not modelled 95.8 11 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from bartonella2 henselae
52d1h5ya_



not modelled 95.7 21 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
53c3e96B_



not modelled 95.7 13 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 bacillus clausii
54d1o5ka_



not modelled 95.7 12 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
55c3noeA_



not modelled 95.6 10 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from pseudomonas2 aeruginosa
56c3daqB_



not modelled 95.6 17 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from methicillin-2 resistant staphylococcus aureus
57c2vc6A_



not modelled 95.5 12 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: structure of mosa from s. meliloti with pyruvate bound
58c3eb2A_



not modelled 95.4 17 PDB header:lyase
Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 rhodopseudomonas palustris at 2.0a resolution
59c2fdsA_



not modelled 95.3 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:orotidine-monophosphate-decarboxylase;
PDBTitle: crystal structure of plasmodium berghei orotidine 5'-2 monophosphate decarboxylase (ortholog of plasmodium3 falciparum pf10_0225)
60d2fdsa1



not modelled 95.3 14 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Decarboxylase
61c3bi8A_



not modelled 95.3 14 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: structure of dihydrodipicolinate synthase from clostridium2 botulinum
62d1xkya1



not modelled 95.1 17 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
63c3na8A_



not modelled 94.9 16 PDB header:lyase
Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase;
PDBTitle: crystal structure of a putative dihydrodipicolinate synthetase from2 pseudomonas aeruginosa
64c3g0sA_



not modelled 94.8 12 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: dihydrodipicolinate synthase from salmonella typhimurium lt2
65c3lerA_



not modelled 94.8 12 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 campylobacter jejuni subsp. jejuni nctc 11168
66c2qw5B_



not modelled 94.8 17 PDB header:isomerase
Chain: B: PDB Molecule:xylose isomerase-like tim barrel;
PDBTitle: crystal structure of a putative sugar phosphate isomerase/epimerase2 (ava4194) from anabaena variabilis atcc 29413 at 1.78 a resolution
67d2a6na1



not modelled 94.7 14 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
68c2qygC_



not modelled 94.5 15 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
69c2oemA_



not modelled 94.3 18 PDB header:isomerase
Chain: A: PDB Molecule:2,3-diketo-5-methylthiopentyl-1-phosphate enolase;
PDBTitle: crystal structure of a rubisco-like protein from geobacillus2 kaustophilus liganded with mg2+ and 2,3-diketohexane 1-phosphate
70c3fluD_



not modelled 94.2 13 PDB header:lyase
Chain: D: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from the pathogen2 neisseria meningitidis
71c6reqB_



not modelled 94.2 14 PDB header:isomerase
Chain: B: PDB Molecule:protein (methylmalonyl-coa mutase);
PDBTitle: methylmalonyl-coa mutase, 3-carboxypropyl-coa inhibitor complex
72d1u1ha2



not modelled 93.8 15 Fold:TIM beta/alpha-barrel
Superfamily:UROD/MetE-like
Family:Cobalamin-independent methionine synthase
73c2nx9B_



not modelled 93.7 18 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
74c3qfwB_



not modelled 93.6 19 PDB header:lyase
Chain: B: PDB Molecule:ribulose-1,5-bisphosphate carboxylase/oxygenase large
PDBTitle: crystal structure of rubisco-like protein from rhodopseudomonas2 palustris
75d2ffca1



not modelled 93.2 14 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Decarboxylase
76c3qfeB_



not modelled 93.2 16 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
77c3cprB_



not modelled 93.2 20 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthetase;
PDBTitle: the crystal structure of corynebacterium glutamicum2 dihydrodipicolinate synthase to 2.2 a resolution
78c2yxgD_



not modelled 92.9 10 PDB header:lyase
Chain: D: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihyrodipicolinate synthase (dapa)
79c2d69B_



not modelled 92.9 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)
80d1jvna1



not modelled 92.7 21 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
81c2rfgB_



not modelled 92.6 17 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from hahella2 chejuensis at 1.5a resolution
82d1vhna_



not modelled 92.4 18 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
83c2y0fD_



not modelled 92.1 20 PDB header:oxidoreductase
Chain: D: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase;
PDBTitle: structure of gcpe (ispg) from thermus thermophilus hb27
84c1jvnB_



not modelled 91.8 19 PDB header:transferase
Chain: B: PDB Molecule:bifunctional histidine biosynthesis protein hishf;
PDBTitle: crystal structure of imidazole glycerol phosphate synthase: a tunnel2 through a (beta/alpha)8 barrel joins two active sites
85c2y85D_



not modelled 91.8 17 PDB header:isomerase
Chain: D: PDB Molecule:phosphoribosyl isomerase a;
PDBTitle: crystal structure of mycobacterium tuberculosis phosphoribosyl2 isomerase with bound rcdrp
86c1telA_



not modelled 91.7 16 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
87d1qh8b_



not modelled 91.7 13 Fold:Chelatase-like
Superfamily:"Helical backbone" metal receptor
Family:Nitrogenase iron-molybdenum protein
88c2r94B_



not modelled 91.7 16 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
89d1ykwa1



not modelled 91.1 16 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
90d2q8za1



not modelled 91.0 12 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Decarboxylase
91d1m1na_



not modelled 91.0 14 Fold:Chelatase-like
Superfamily:"Helical backbone" metal receptor
Family:Nitrogenase iron-molybdenum protein
92d1hl2a_



not modelled 90.8 10 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
93d2d69a1



not modelled 90.7 17 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
94c3obkH_



not modelled 90.7 18 PDB header:lyase
Chain: H: PDB Molecule:delta-aminolevulinic acid dehydratase;
PDBTitle: crystal structure of delta-aminolevulinic acid dehydratase2 (porphobilinogen synthase) from toxoplasma gondii me49 in complex3 with the reaction product porphobilinogen
95c3d0cB_



not modelled 90.5 11 PDB header:lyase
Chain: B: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 oceanobacillus iheyensis at 1.9 a resolution
96d1thfd_



not modelled 90.2 14 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
97c3dz1A_



not modelled 90.1 16 PDB header:lyase
Chain: A: PDB Molecule:dihydrodipicolinate synthase;
PDBTitle: crystal structure of dihydrodipicolinate synthase from2 rhodopseudomonas palustris at 1.87a resolution
98d1f74a_



not modelled 89.7 13 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
99d1m1nb_



not modelled 89.6 13 Fold:Chelatase-like
Superfamily:"Helical backbone" metal receptor
Family:Nitrogenase iron-molybdenum protein
100d1rd5a_



not modelled 89.5 14 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
101d7reqb2



not modelled 89.3 17 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
102c3r89A_



not modelled 89.2 16 PDB header:lyase
Chain: A: PDB Molecule:orotidine 5'-phosphate decarboxylase;
PDBTitle: crystal structure of orotidine 5-phosphate decarboxylase from2 anaerococcus prevotii dsm 20548
103c3eooL_



not modelled 89.2 23 PDB header:lyase
Chain: L: PDB Molecule:methylisocitrate lyase;
PDBTitle: 2.9a crystal structure of methyl-isocitrate lyase from2 burkholderia pseudomallei
104d1muma_



not modelled 89.2 18 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like
105d8ruca1



not modelled 89.1 12 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
106c3pueA_



not modelled 89.0 15 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
107d1o66a_



not modelled 88.6 17 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Ketopantoate hydroxymethyltransferase PanB
108c3b0vD_



not modelled 88.4 17 PDB header:oxidoreductase/rna
Chain: D: PDB Molecule:trna-dihydrouridine synthase;
PDBTitle: trna-dihydrouridine synthase from thermus thermophilus in complex with2 trna
109c3qw3B_



not modelled 87.8 16 PDB header:transferase, lyase
Chain: B: PDB Molecule:orotidine-5-phosphate decarboxylase/orotate
PDBTitle: structure of leishmania donovani omp decarboxylase
110c3nwrA_



not modelled 87.3 17 PDB header:lyase
Chain: A: PDB Molecule:a rubisco-like protein;
PDBTitle: crystal structure of a rubisco-like protein from burkholderia fungorum
111c3lciA_



not modelled 86.6 13 PDB header:lyase
Chain: A: PDB Molecule:n-acetylneuraminate lyase;
PDBTitle: the d-sialic acid aldolase mutant v251w
112c1rldB_



not modelled 86.5 21 PDB header:lyase(carbon-carbon)
Chain: B: PDB Molecule:ribulose 1,5 bisphosphate carboxylase/oxygenase (large
PDBTitle: solid-state phase transition in the crystal structure of ribulose 1,5-2 biphosphate carboxylase(slash)oxygenase
113d1wdda1



not modelled 86.2 15 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
114c3lmaC_



not modelled 85.9 19 PDB header:membrane protein
Chain: C: PDB Molecule:stage v sporulation protein ad (spovad);
PDBTitle: crystal structure of the stage v sporulation protein ad2 (spovad) from bacillus licheniformis. northeast structural3 genomics consortium target bir6.
115c3ru6C_



not modelled 85.8 10 PDB header:lyase
Chain: C: PDB Molecule:orotidine 5'-phosphate decarboxylase;
PDBTitle: 1.8 angstrom resolution crystal structure of orotidine 5'-phosphate2 decarboxylase (pyrf) from campylobacter jejuni subsp. jejuni nctc3 11168
116d1vzwa1



not modelled 85.7 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
117c1rcxH_



not modelled 85.6 12 PDB header:lyase (carbon-carbon)
Chain: H: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase;
PDBTitle: non-activated spinach rubisco in complex with its substrate2 ribulose-1,5-bisphosphate
118c1ypxA_



not modelled 85.4 13 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
119c3lyeA_



not modelled 84.9 15 PDB header:hydrolase
Chain: A: PDB Molecule:oxaloacetate acetyl hydrolase;
PDBTitle: crystal structure of oxaloacetate acetylhydrolase
120c2ftpA_



not modelled 84.3 13 PDB header:lyase
Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase;
PDBTitle: crystal structure of hydroxymethylglutaryl-coa lyase from pseudomonas2 aeruginosa

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