Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AEI1
DateThu Jan 5 11:23:24 GMT 2012
Unique Job IDc8fc6f0e5d14603f

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2qgqF_
Top template information
PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:protein tm_1862;
PDBTitle: crystal structure of tm_1862 from thermotoga maritima.2 northeast structural genomics consortium target vr77
Confidence and coverage
Confidence:100.0% Coverage: 56%
264 residues ( 56% 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.
381 residues ( 80%) 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  MTKKLHIKTWGCQMNEYDSSKMADLLDATHGYQLTDVAEEADVLLLNTCSIREKAQEKVF
Secondary structure 
SS confidence 
Disorder  ???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  HQLGRWKLLKEKNPDLIIGVGGCVASQEGEHIRQRAHYVDIIFGPQTLHRLPEMINSVRG
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  DRSPVVDISFPEIEKFDRLPEPRAEGPTAFVSIMEGCNKYCTYCVVPYTRGEEVSRPSDD
Secondary structure 
SS confidence 
Disorder 
??????
??
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  ILFEIAQLAAQGVREVNLLGQNVNAWRGENYDGTTGSFADLLRLVAAIDGIDRIRFTTSH
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  PIEFTDDIIEVYRDTPELVSFLHLPVQSGSDRILNLMGRTHTALEYKAIIRKLRAARPDI
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  QISSDFIVGFPGETTEDFEKTMKLIADVNFDMSYSFIFSARPGTPAADMVDDVPEEEKKQ
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  RLYILQERINQQAMAWSRRMLGTTQRILVEGTSRKSIMELSGRTENNRVVNFEGTPDMIG
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470....
Sequence  KFVDVEITDVYPNSLRGKVVRTEDEMGLRVAETPESVIARTRKENDLGVGYYQP
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 2qgq chain F

3D model

Region: 161 - 440
Aligned: 264
Modelled: 280
Confidence: 100.0%
Identity: 32%
PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:protein tm_1862;
PDBTitle: crystal structure of tm_1862 from thermotoga maritima.2 northeast structural genomics consortium target vr77

Phyre2

PDB 3cix chain A

3D model

Region: 148 - 366
Aligned: 201
Modelled: 219
Confidence: 100.0%
Identity: 15%
PDB header:adomet binding protein
Chain: A: PDB Molecule:fefe-hydrogenase maturase;
PDBTitle: x-ray structure of the [fefe]-hydrogenase maturase hyde from2 thermotoga maritima in complex with thiocyanate

Phyre2

PDB 1olt chain A

3D model

Region: 124 - 375
Aligned: 240
Modelled: 242
Confidence: 100.0%
Identity: 19%
Fold: TIM beta/alpha-barrel
Superfamily: Radical SAM enzymes
Family: Oxygen-independent coproporphyrinogen III oxidase HemN

Phyre2

PDB 3t7v chain A

3D model

Region: 147 - 359
Aligned: 199
Modelled: 213
Confidence: 99.9%
Identity: 16%
PDB header:transferase
Chain: A: PDB Molecule:methylornithine synthase pylb;
PDBTitle: crystal structure of methylornithine synthase (pylb)

Phyre2

PDB 1r30 chain A

3D model

Region: 148 - 366
Aligned: 202
Modelled: 214
Confidence: 99.9%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:biotin synthase;
PDBTitle: the crystal structure of biotin synthase, an s-2 adenosylmethionine-dependent radical enzyme

Phyre2

PDB 1r30 chain A

3D model

Region: 148 - 366
Aligned: 202
Modelled: 219
Confidence: 99.9%
Identity: 20%
Fold: TIM beta/alpha-barrel
Superfamily: Radical SAM enzymes
Family: Biotin synthase

Phyre2

PDB 3rfa chain A

3D model

Region: 142 - 367
Aligned: 211
Modelled: 226
Confidence: 99.8%
Identity: 13%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribosomal rna large subunit methyltransferase n;
PDBTitle: x-ray structure of rlmn from escherichia coli in complex with s-2 adenosylmethionine

Phyre2

PDB 2yx0 chain A

3D model

Region: 151 - 367
Aligned: 201
Modelled: 214
Confidence: 99.7%
Identity: 13%
PDB header:metal binding protein
Chain: A: PDB Molecule:radical sam enzyme;
PDBTitle: crystal structure of p. horikoshii tyw1

Phyre2

PDB 1tv8 chain A

3D model

Region: 147 - 365
Aligned: 202
Modelled: 219
Confidence: 99.6%
Identity: 16%
Fold: TIM beta/alpha-barrel
Superfamily: Radical SAM enzymes
Family: MoCo biosynthesis proteins

Phyre2

PDB 2a5h chain C

3D model

Region: 146 - 350
Aligned: 185
Modelled: 200
Confidence: 99.5%
Identity: 15%
PDB header:isomerase
Chain: C: PDB Molecule:l-lysine 2,3-aminomutase;
PDBTitle: 2.1 angstrom x-ray crystal structure of lysine-2,3-aminomutase from2 clostridium subterminale sb4, with michaelis analog (l-alpha-lysine3 external aldimine form of pyridoxal-5'-phosphate).

Phyre2

PDB 3c8f chain A

3D model

Region: 130 - 371
Aligned: 226
Modelled: 231
Confidence: 99.5%
Identity: 13%
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate formate-lyase 1-activating enzyme;
PDBTitle: 4fe-4s-pyruvate formate-lyase activating enzyme with2 partially disordered adomet

Phyre2

PDB 2z2u chain A

3D model

Region: 157 - 342
Aligned: 161
Modelled: 182
Confidence: 97.4%
Identity: 10%
PDB header:metal binding protein
Chain: A: PDB Molecule:upf0026 protein mj0257;
PDBTitle: crystal structure of archaeal tyw1

Phyre2

PDB 3can chain A

3D model

Region: 196 - 371
Aligned: 147
Modelled: 175
Confidence: 97.1%
Identity: 14%
PDB header:lyase activator
Chain: A: PDB Molecule:pyruvate-formate lyase-activating enzyme;
PDBTitle: crystal structure of a domain of pyruvate-formate lyase-activating2 enzyme from bacteroides vulgatus atcc 8482

Phyre2

PDB 2ftp chain A

3D model

Region: 175 - 335
Aligned: 148
Modelled: 161
Confidence: 96.4%
Identity: 8%
PDB header:lyase
Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase;
PDBTitle: crystal structure of hydroxymethylglutaryl-coa lyase from pseudomonas2 aeruginosa

Phyre2

PDB 3bul chain A domain 2

3D model

Region: 21 - 122
Aligned: 97
Modelled: 102
Confidence: 95.3%
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: 4 - 120
Aligned: 109
Modelled: 117
Confidence: 95.2%
Identity: 19%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2

PDB 1yvc chain A domain 1

3D model

Region: 381 - 440
Aligned: 55
Modelled: 60
Confidence: 95.0%
Identity: 18%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: TRAM domain

Phyre2

PDB 1yez chain A domain 1

3D model

Region: 381 - 441
Aligned: 56
Modelled: 61
Confidence: 95.0%
Identity: 21%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: TRAM domain

Phyre2

PDB 1bmt chain B

3D model

Region: 21 - 123
Aligned: 98
Modelled: 103
Confidence: 94.9%
Identity: 16%
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 2cw6 chain B

3D model

Region: 175 - 335
Aligned: 148
Modelled: 161
Confidence: 94.8%
Identity: 11%
PDB header:lyase
Chain: B: PDB Molecule:hydroxymethylglutaryl-coa lyase, mitochondrial;
PDBTitle: crystal structure of human hmg-coa lyase: insights into2 catalysis and the molecular basis for3 hydroxymethylglutaric aciduria

Phyre2

PDB 1y80 chain A

3D model

Region: 21 - 118
Aligned: 87
Modelled: 87
Confidence: 93.9%
Identity: 14%
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 1e1c chain A

3D model

Region: 4 - 121
Aligned: 110
Modelled: 110
Confidence: 92.5%
Identity: 18%
PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant

Phyre2

PDB 1ccw chain A

3D model

Region: 1 - 122
Aligned: 116
Modelled: 116
Confidence: 92.1%
Identity: 14%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2
1
c2qgqF_
2
c3cixA_
3
d1olta_
4
c3t7vA_
5
c1r30A_
6
d1r30a_
7
c3rfaA_
8
c2yx0A_
9
d1tv8a_
10
c2a5hC_
11
c3c8fA_
12
c2z2uA_
13
c3canA_
14
c2ftpA_
15
d3bula2
16
d7reqa2
17
d1yvca1
18
d1yeza1
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c1bmtB_
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c2cw6B_
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c1y80A_
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c1e1cA_
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d1ccwa_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2qgqF_
100.0 32 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:protein tm_1862;
PDBTitle: crystal structure of tm_1862 from thermotoga maritima.2 northeast structural genomics consortium target vr77
2c3cixA_
100.0 15 PDB header:adomet binding protein
Chain: A: PDB Molecule:fefe-hydrogenase maturase;
PDBTitle: x-ray structure of the [fefe]-hydrogenase maturase hyde from2 thermotoga maritima in complex with thiocyanate
3d1olta_
100.0 19 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:Oxygen-independent coproporphyrinogen III oxidase HemN
4c3t7vA_
99.9 16 PDB header:transferase
Chain: A: PDB Molecule:methylornithine synthase pylb;
PDBTitle: crystal structure of methylornithine synthase (pylb)
5c1r30A_
99.9 20 PDB header:transferase
Chain: A: PDB Molecule:biotin synthase;
PDBTitle: the crystal structure of biotin synthase, an s-2 adenosylmethionine-dependent radical enzyme
6d1r30a_
99.9 20 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:Biotin synthase
7c3rfaA_
99.8 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribosomal rna large subunit methyltransferase n;
PDBTitle: x-ray structure of rlmn from escherichia coli in complex with s-2 adenosylmethionine
8c2yx0A_
99.7 13 PDB header:metal binding protein
Chain: A: PDB Molecule:radical sam enzyme;
PDBTitle: crystal structure of p. horikoshii tyw1
9d1tv8a_
99.6 16 Fold:TIM beta/alpha-barrel
Superfamily:Radical SAM enzymes
Family:MoCo biosynthesis proteins
10c2a5hC_
99.5 15 PDB header:isomerase
Chain: C: PDB Molecule:l-lysine 2,3-aminomutase;
PDBTitle: 2.1 angstrom x-ray crystal structure of lysine-2,3-aminomutase from2 clostridium subterminale sb4, with michaelis analog (l-alpha-lysine3 external aldimine form of pyridoxal-5'-phosphate).
11c3c8fA_
99.5 13 PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate formate-lyase 1-activating enzyme;
PDBTitle: 4fe-4s-pyruvate formate-lyase activating enzyme with2 partially disordered adomet
12c2z2uA_
97.4 10 PDB header:metal binding protein
Chain: A: PDB Molecule:upf0026 protein mj0257;
PDBTitle: crystal structure of archaeal tyw1
13c3canA_
97.1 14 PDB header:lyase activator
Chain: A: PDB Molecule:pyruvate-formate lyase-activating enzyme;
PDBTitle: crystal structure of a domain of pyruvate-formate lyase-activating2 enzyme from bacteroides vulgatus atcc 8482
14c2ftpA_
96.4 8 PDB header:lyase
Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase;
PDBTitle: crystal structure of hydroxymethylglutaryl-coa lyase from pseudomonas2 aeruginosa
15d3bula2
95.3 16 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
16d7reqa2
95.2 19 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
17d1yvca1
95.0 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
18d1yeza1
95.0 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
19c1bmtB_
94.9 16 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
20c2cw6B_
94.8 11 PDB header:lyase
Chain: B: PDB Molecule:hydroxymethylglutaryl-coa lyase, mitochondrial;
PDBTitle: crystal structure of human hmg-coa lyase: insights into2 catalysis and the molecular basis for3 hydroxymethylglutaric aciduria
21d1uwva1
not modelled 94.4 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
22c1uwvA_
not modelled 94.3 19 PDB header:transferase
Chain: A: PDB Molecule:23s rrna (uracil-5-)-methyltransferase ruma;
PDBTitle: crystal structure of ruma, the iron-sulfur cluster2 containing e. coli 23s ribosomal rna 5-methyluridine3 methyltransferase
23c3ivuB_
not modelled 94.3 11 PDB header:transferase
Chain: B: PDB Molecule:homocitrate synthase, mitochondrial;
PDBTitle: homocitrate synthase lys4 bound to 2-og
24c1y80A_
93.9 14 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
25d1f6ya_
not modelled 93.9 9 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Methyltetrahydrofolate-utiluzing methyltransferases
26c3eegB_
not modelled 93.2 11 PDB header:transferase
Chain: B: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of a 2-isopropylmalate synthase from2 cytophaga hutchinsonii
27c1ydnA_
not modelled 93.0 9 PDB header:lyase
Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase;
PDBTitle: crystal structure of the hmg-coa lyase from brucella melitensis,2 northeast structural genomics target lr35.
28c3ewbX_
not modelled 92.8 10 PDB header:transferase
Chain: X: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of n-terminal domain of putative 2-2 isopropylmalate synthase from listeria monocytogenes
29d1qt1a_
not modelled 92.5 13 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
30c1e1cA_
92.5 18 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant
31d1nvma2
not modelled 92.5 13 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:HMGL-like
32d1ccwa_
92.1 14 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
33c1nvmG_
not modelled 91.5 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
34c1tx2A_
not modelled 90.9 17 PDB header:transferase
Chain: A: PDB Molecule:dhps, dihydropteroate synthase;
PDBTitle: dihydropteroate synthetase, with bound inhibitor manic, from bacillus2 anthracis
35d1tx2a_
not modelled 90.9 17 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
36c2vs1A_
not modelled 90.9 11 PDB header:transferase
Chain: A: PDB Molecule:uncharacterized rna methyltransferase pyrab10780;
PDBTitle: the crystal structure of pyrococcus abyssi trna (uracil-54,2 c5)-methyltransferase in complex with s-adenosyl-l-3 homocysteine
37c2p10D_
not modelled 90.8 22 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
38d1muwa_
not modelled 90.6 13 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
39c3ezxA_
not modelled 90.1 21 PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein
40c2yciX_
not modelled 88.9 15 PDB header:transferase
Chain: X: PDB Molecule:5-methyltetrahydrofolate corrinoid/iron sulfur protein
PDBTitle: methyltransferase native
41c3khdC_
not modelled 88.4 12 PDB header:transferase
Chain: C: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pff1300w.
42d1fmfa_
not modelled 88.4 18 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
43d1xima_
not modelled 87.8 9 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
44c3bleA_
not modelled 85.6 12 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
45c3hpxB_
not modelled 85.3 14 PDB header:transferase
Chain: B: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of mycobacterium tuberculosis leua active site2 domain 1-425 (truncation mutant delta:426-644)
46d2glka1
not modelled 84.6 12 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
47c1zfjA_
not modelled 83.5 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:inosine monophosphate dehydrogenase;
PDBTitle: inosine monophosphate dehydrogenase (impdh; ec 1.1.1.205) from2 streptococcus pyogenes
48c3tr9A_
not modelled 83.1 15 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase;
PDBTitle: structure of a dihydropteroate synthase (folp) in complex with pteroic2 acid from coxiella burnetii
49c2bdqA_
not modelled 82.2 13 PDB header:metal transport
Chain: A: PDB Molecule:copper homeostasis protein cutc;
PDBTitle: crystal structure of the putative copper homeostasis2 protein cutc from streptococcus agalactiae, northeast3 strucural genomics target sar15.
50c2i2xD_
not modelled 81.6 23 PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri
51c2yxbA_
not modelled 81.6 19 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
52c1k98A_
not modelled 81.6 16 PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment
53d1ad1a_
not modelled 81.0 15 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
54c2hk1D_
not modelled 81.0 12 PDB header:isomerase
Chain: D: PDB Molecule:d-psicose 3-epimerase;
PDBTitle: crystal structure of d-psicose 3-epimerase (dpease) in the presence of2 d-fructose
55d1h4pa_
not modelled 80.7 11 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
56d1eyea_
not modelled 79.8 14 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
57c3ct7E_
not modelled 77.4 14 PDB header:isomerase
Chain: E: PDB Molecule:d-allulose-6-phosphate 3-epimerase;
PDBTitle: crystal structure of d-allulose 6-phosphate 3-epimerase2 from escherichia coli k-12
58d1mxsa_
not modelled 76.6 16 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
59d3bofa1
not modelled 76.5 11 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Methyltetrahydrofolate-utiluzing methyltransferases
60d1xrsb1
not modelled 76.1 20 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
61d1k77a_
not modelled 76.1 12 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Hypothetical protein YgbM (EC1530)
62c2yw3E_
not modelled 76.0 18 PDB header:lyase
Chain: E: PDB Molecule:4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-
PDBTitle: crystal structure analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-2 deydro-3-deoxyphosphogluconate aldolase from tthb1
63d1vhca_
not modelled 74.6 20 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
64c3no5C_
not modelled 74.3 12 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a pfam duf849 domain containing protein2 (reut_a1631) from ralstonia eutropha jmp134 at 1.90 a resolution
65d1pkla2
not modelled 74.3 16 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
66c3lu2B_
not modelled 74.0 22 PDB header:hydrolase
Chain: B: PDB Molecule:lmo2462 protein;
PDBTitle: structure of lmo2462, a listeria monocytogenes amidohydrolase family2 putative dipeptidase
67d1ajza_
not modelled 73.6 16 Fold:TIM beta/alpha-barrel
Superfamily:Dihydropteroate synthetase-like
Family:Dihydropteroate synthetase
68c3bicA_
not modelled 73.6 17 PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase, mitochondrial precursor;
PDBTitle: crystal structure of human methylmalonyl-coa mutase
69d2fiqa1
not modelled 72.8 17 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:GatZ-like
70c1sr9A_
not modelled 71.0 13 PDB header:transferase
Chain: A: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of leua from mycobacterium tuberculosis
71d1xlma_
not modelled 70.8 11 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
72c6reqB_
not modelled 70.6 17 PDB header:isomerase
Chain: B: PDB Molecule:protein (methylmalonyl-coa mutase);
PDBTitle: methylmalonyl-coa mutase, 3-carboxypropyl-coa inhibitor complex
73d1x7fa2
not modelled 69.9 18 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Outer surface protein, N-terminal domain
74c3npgD_
not modelled 69.2 15 PDB header:unknown function
Chain: D: PDB Molecule:uncharacterized duf364 family protein;
PDBTitle: crystal structure of a protein with unknown function from duf3642 family (ph1506) from pyrococcus horikoshii at 2.70 a resolution
75c3bolB_
not modelled 68.8 11 PDB header:transferase
Chain: B: PDB Molecule:5-methyltetrahydrofolate s-homocysteine
PDBTitle: cobalamin-dependent methionine synthase (1-566) from2 thermotoga maritima complexed with zn2+
76d2h1qa1
not modelled 68.4 21 Fold:PLP-dependent transferase-like
Superfamily:Dhaf3308-like
Family:Dhaf3308-like
77c3itcA_
not modelled 68.0 25 PDB header:hydrolase
Chain: A: PDB Molecule:renal dipeptidase;
PDBTitle: crystal structure of sco3058 with bound citrate and glycerol
78d1tqxa_
not modelled 66.9 18 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:D-ribulose-5-phosphate 3-epimerase
79c3r79B_
not modelled 66.4 11 PDB header:structure genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of an uncharactertized protein from agrobacterium2 tumefaciens
80c3labA_
not modelled 65.6 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative kdpg (2-keto-3-deoxy-6-phosphogluconate)
PDBTitle: crystal structure of a putative kdpg (2-keto-3-deoxy-6-2 phosphogluconate) aldolase from oleispira antarctica
81c1ydoC_
not modelled 65.3 10 PDB header:lyase
Chain: C: PDB Molecule:hmg-coa lyase;
PDBTitle: crystal structure of the bacillis subtilis hmg-coa lyase, northeast2 structural genomics target sr181.
82d1qopa_
not modelled 65.3 17 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
83d1wbha1
not modelled 65.2 18 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
84d1itua_
not modelled 64.7 18 Fold:TIM beta/alpha-barrel
Superfamily:Metallo-dependent hydrolases
Family:Renal dipeptidase
85c3fdgA_
not modelled 63.3 17 PDB header:hydrolase
Chain: A: PDB Molecule:dipeptidase ac. metallo peptidase. merops family m19;
PDBTitle: the crystal structure of the dipeptidase ac, metallo peptidase. merops2 family m19
86c1x7fA_
not modelled 63.1 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:outer surface protein;
PDBTitle: crystal structure of an uncharacterized b. cereus protein
87d1liua2
not modelled 62.8 10 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
88d1e0ta2
not modelled 62.6 10 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
89d1mvoa_
not modelled 62.5 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
90d1bxca_
not modelled 61.3 12 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
91c2vefB_
not modelled 60.4 17 PDB header:transferase
Chain: B: PDB Molecule:dihydropteroate synthase;
PDBTitle: dihydropteroate synthase from streptococcus pneumoniae
92c3ngfA_
not modelled 60.4 13 PDB header:isomerase
Chain: A: PDB Molecule:ap endonuclease, family 2;
PDBTitle: crystal structure of ap endonuclease, family 2 from brucella2 melitensis
93c2qs0A_
not modelled 60.2 20 PDB header:biosynthetic protein
Chain: A: PDB Molecule:quinolinate synthetase a;
PDBTitle: quinolinate synthase from pyrococcus furiosus
94c1u5tA_
not modelled 60.0 19 PDB header:transport protein
Chain: A: PDB Molecule:appears to be functionally related to snf7;
PDBTitle: structure of the escrt-ii endosomal trafficking complex
95d1gvia3
not modelled 59.4 15 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
96c2zyfA_
not modelled 59.1 13 PDB header:transferase
Chain: A: PDB Molecule:homocitrate synthase;
PDBTitle: crystal structure of homocitrate synthase from thermus thermophilus2 complexed with magnesuim ion and alpha-ketoglutarate
97c2xvzA_
not modelled 56.6 20 PDB header:metal binding protein
Chain: A: PDB Molecule:chelatase, putative;
PDBTitle: cobalt chelatase cbik (periplasmatic) from desulvobrio2 vulgaris hildenborough (co-crystallized with cobalt)
98c3cqkB_
not modelled 56.1 12 PDB header:isomerase
Chain: B: PDB Molecule:l-ribulose-5-phosphate 3-epimerase ulae;
PDBTitle: crystal structure of l-xylulose-5-phosphate 3-epimerase ulae (form b)2 complex with zn2+ and sulfate
99c3chvA_
not modelled 55.3 11 PDB header:metal binding protein
Chain: A: PDB Molecule:prokaryotic domain of unknown function (duf849) with a tim
PDBTitle: crystal structure of a prokaryotic domain of unknown function (duf849)2 member (spoa0042) from silicibacter pomeroyi dss-3 at 1.45 a3 resolution
100d1mkza_
not modelled 55.2 21 Fold:Molybdenum cofactor biosynthesis proteins
Superfamily:Molybdenum cofactor biosynthesis proteins
Family:MogA-like
101c2vp8A_
not modelled 55.1 16 PDB header:transferase
Chain: A: PDB Molecule:dihydropteroate synthase 2;
PDBTitle: structure of mycobacterium tuberculosis rv1207
102d1h1ya_
not modelled 55.0 8 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:D-ribulose-5-phosphate 3-epimerase
103c1xrsB_
not modelled 54.6 18 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
104d1a3xa2
not modelled 54.2 14 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
105d1m7xa3
not modelled 53.1 23 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
106d2pb1a1
not modelled 52.9 17 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
107c3dx5A_
not modelled 52.9 8 PDB header:lyase
Chain: A: PDB Molecule:uncharacterized protein asbf;
PDBTitle: crystal structure of the probable 3-dhs dehydratase asbf involved in2 the petrobactin synthesis from bacillus anthracis
108c3elbA_
not modelled 52.2 17 PDB header:transferase
Chain: A: PDB Molecule:ethanolamine-phosphate cytidylyltransferase;
PDBTitle: human ctp: phosphoethanolamine cytidylyltransferase in complex with2 cmp
109c3zu0A_
not modelled 50.8 21 PDB header:hydrolase
Chain: A: PDB Molecule:nad nucleotidase;
PDBTitle: structure of haemophilus influenzae nad nucleotidase (nadn)
110d7reqb2
not modelled 50.6 14 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
111c2i5gB_
not modelled 50.2 16 PDB header:hydrolase
Chain: B: PDB Molecule:amidohydrolase;
PDBTitle: crystal strcuture of amidohydrolase from pseudomonas2 aeruginosa
112d1yx1a1
not modelled 49.0 7 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:KguE-like
113c3k1dA_
not modelled 48.7 19 PDB header:transferase
Chain: A: PDB Molecule:1,4-alpha-glucan-branching enzyme;
PDBTitle: crystal structure of glycogen branching enzyme synonym: 1,4-alpha-d-2 glucan:1,4-alpha-d-glucan 6-glucosyl-transferase from mycobacterium3 tuberculosis h37rv
114c3pdiG_
not modelled 48.5 20 PDB header:protein binding
Chain: G: PDB Molecule:nitrogenase mofe cofactor biosynthesis protein nife;
PDBTitle: precursor bound nifen
115c1l2fA_
not modelled 48.3 19 PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain
116c3dhuC_
not modelled 47.9 14 PDB header:hydrolase
Chain: C: PDB Molecule:alpha-amylase;
PDBTitle: crystal structure of an alpha-amylase from lactobacillus2 plantarum
117d1u2za_
not modelled 47.9 34 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:Catalytic, N-terminal domain of histone methyltransferase Dot1l
118d1o4ua1
not modelled 47.8 24 Fold:TIM beta/alpha-barrel
Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like
Family:NadC C-terminal domain-like
119c2d4aC_
not modelled 47.5 17 PDB header:oxidoreductase
Chain: C: PDB Molecule:malate dehydrogenase;
PDBTitle: structure of the malate dehydrogenase from aeropyrum pernix
120c3pdiB_
not modelled 46.6 20 PDB header:protein binding
Chain: B: PDB Molecule:nitrogenase mofe cofactor biosynthesis protein nifn;
PDBTitle: precursor bound nifen

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