Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP33363
DateThu Jan 5 11:52:06 GMT 2012
Unique Job IDf44e8a91bf2644fb

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3ac0B_
Top template information
PDB header:hydrolase
Chain: B: PDB Molecule:beta-glucosidase i;
PDBTitle: crystal structure of beta-glucosidase from kluyveromyces marxianus in2 complex with glucose
Confidence and coverage
Confidence:100.0% Coverage: 86%
661 residues ( 86% 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.
740 residues ( 97%) 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  MKWLCSVGIAVSLALQPALADDLFGNHPLTPEARDAFVTELLKKMTVDEKIGQLRLISVG
Secondary structure 
SS confidence 
Disorder  ???
??????????
???
??
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  PDNPKEAIREMIKDGQVGAIFNTVTRQDIRAMQDQVMELSRLKIPLFFAYDVLHGQRTVF
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  PISLGLASSFNLDAVKTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  TSTMGKTMVEAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSPQRLFNDYMPPY
Secondary structure 
SS confidence 
Disorder 
????
????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  KAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDQWGFKGITVSDHGAIKELIKHGTA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  ADPEDAVRVALKSGINMSMSDEYYSKYLPGLIKSGKVTMAELDDAARHVLNVKYDMGLFN
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  DPYSHLGPKESDPVDTNAESRLHRKEAREVARESLVLLKNRLETLPLKKSATIAVVGPLA
Secondary structure 
SS confidence 
Disorder 
????
????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  DSKRDVMGSWSAAGVADQSVTVLTGIKNAVGENGKVLYAKGANVTSDKGIIDFLNQYEEA
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  VKVDPRSPQEMIDEAVQTAKQSDVVVAVVGEAQGMAHEASSRTDITIPQSQRDLIAALKA
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  TGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPMSFP
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  RSVGQIPVYYSHLNTGRPYNADKPNKYTSRYFDEANGALYPFGYGLSYTTFTVSDVKLSA
Secondary structure 
SS confidence 
Disorder 
?
?
??
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  PTMKRDGKVTASVQVTNTGKREGATVVQMYLQDVTASMSRPVKQLKGFEKITLKPGETQT
Secondary structure 
SS confidence 
Disorder  ????
?
?????
Disorder confidence 
 
   .........730.........740.........750.........760.....
Sequence  VSFPIDIEALKFWNQQMKYDAEPGKFNVFIGTDSARVKKGEFELL
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 3ac0 chain B

3D model

Region: 38 - 764
Aligned: 661
Modelled: 672
Confidence: 100.0%
Identity: 33%
PDB header:hydrolase
Chain: B: PDB Molecule:beta-glucosidase i;
PDBTitle: crystal structure of beta-glucosidase from kluyveromyces marxianus in2 complex with glucose

Phyre2

PDB 2x41 chain A

3D model

Region: 37 - 764
Aligned: 671
Modelled: 690
Confidence: 100.0%
Identity: 30%
PDB header:hydrolase
Chain: A: PDB Molecule:beta-glucosidase;
PDBTitle: structure of beta-glucosidase 3b from thermotoga neapolitana2 in complex with glucose

Phyre2

PDB 3f93 chain D

3D model

Region: 23 - 764
Aligned: 668
Modelled: 687
Confidence: 100.0%
Identity: 27%
PDB header:hydrolase
Chain: D: PDB Molecule:beta-glucosidase;
PDBTitle: crystal structure of exo-1,3/1,4-beta-glucanase (exop) from2 pseudoalteromonas sp. bb1

Phyre2

PDB 1ex1 chain A

3D model

Region: 23 - 650
Aligned: 557
Modelled: 581
Confidence: 100.0%
Identity: 33%
PDB header:hydrolase
Chain: A: PDB Molecule:protein (beta-d-glucan exohydrolase isoenzyme exo1);
PDBTitle: beta-d-glucan exohydrolase from barley

Phyre2

PDB 3bmx chain B

3D model

Region: 29 - 651
Aligned: 544
Modelled: 549
Confidence: 100.0%
Identity: 25%
PDB header:hydrolase
Chain: B: PDB Molecule:uncharacterized lipoprotein ybbd;
PDBTitle: beta-n-hexosaminidase (ybbd) from bacillus subtilis

Phyre2

PDB 3lk6 chain A

3D model

Region: 32 - 651
Aligned: 541
Modelled: 546
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:lipoprotein ybbd;
PDBTitle: beta-n-hexosaminidase n318d mutant (ybbd_n318d) from bacillus subtilis

Phyre2

PDB 3sql chain B

3D model

Region: 42 - 591
Aligned: 476
Modelled: 487
Confidence: 100.0%
Identity: 20%
PDB header:hydrolase
Chain: B: PDB Molecule:glycosyl hydrolase family 3;
PDBTitle: crystal structure of glycoside hydrolase from synechococcus

Phyre2

PDB 1x38 chain A domain 1

3D model

Region: 22 - 394
Aligned: 356
Modelled: 373
Confidence: 100.0%
Identity: 32%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: NagZ-like

Phyre2

PDB 3tev chain A

3D model

Region: 43 - 356
Aligned: 294
Modelled: 314
Confidence: 100.0%
Identity: 19%
PDB header:hydrolase
Chain: A: PDB Molecule:glycosyl hyrolase, family 3;
PDBTitle: the crystal structure of glycosyl hydrolase from deinococcus2 radiodurans r1

Phyre2

PDB 1tr9 chain A

3D model

Region: 51 - 355
Aligned: 290
Modelled: 300
Confidence: 100.0%
Identity: 22%
Fold: TIM beta/alpha-barrel
Superfamily: (Trans)glycosidases
Family: NagZ-like

Phyre2

PDB 1x38 chain A domain 2

3D model

Region: 395 - 650
Aligned: 202
Modelled: 209
Confidence: 100.0%
Identity: 35%
Fold: Flavodoxin-like
Superfamily: Beta-D-glucan exohydrolase, C-terminal domain
Family: Beta-D-glucan exohydrolase, C-terminal domain

Phyre2

PDB 2kl6 chain A

3D model

Region: 652 - 750
Aligned: 76
Modelled: 86
Confidence: 97.4%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution nmr structure of the cardb domain of pf1109 from2 pyrococcus furiosus. northeast structural genomics3 consortium target pfr193a

Phyre2

PDB 1w8o chain A domain 1

3D model

Region: 656 - 764
Aligned: 91
Modelled: 109
Confidence: 97.3%
Identity: 19%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: E set domains
Family: E-set domains of sugar-utilizing enzymes

Phyre2

PDB 2l0d chain A

3D model

Region: 657 - 756
Aligned: 78
Modelled: 100
Confidence: 97.1%
Identity: 14%
PDB header:cell adhesion
Chain: A: PDB Molecule:cell surface protein;
PDBTitle: solution nmr structure of putative cell surface protein ma_4588 (272-2 376 domain) from methanosarcina acetivorans, northeast structural3 genomics consortium target mvr254a

Phyre2

PDB 2kut chain A

3D model

Region: 656 - 750
Aligned: 84
Modelled: 95
Confidence: 96.9%
Identity: 24%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution structure of gmr58a from geobacter metallireducens.2 northeast structural genomics consortium target gmr58a

Phyre2

PDB 2vzs chain A domain 2

3D model

Region: 655 - 730
Aligned: 74
Modelled: 75
Confidence: 96.2%
Identity: 27%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: beta-Galactosidase/glucuronidase domain
Family: beta-Galactosidase/glucuronidase domain

Phyre2

PDB 1l9m chain B

3D model

Region: 660 - 729
Aligned: 69
Modelled: 70
Confidence: 95.9%
Identity: 14%
PDB header:transferase
Chain: B: PDB Molecule:protein-glutamine glutamyltransferase e3;
PDBTitle: three-dimensional structure of the human transglutaminase 32 enzyme: binding of calcium ions change structure for3 activation

Phyre2

PDB 2q3z chain A domain 2

3D model

Region: 656 - 729
Aligned: 73
Modelled: 74
Confidence: 95.8%
Identity: 16%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: Transglutaminase, two C-terminal domains
Family: Transglutaminase, two C-terminal domains

Phyre2

PDB 2x3b chain B

3D model

Region: 655 - 754
Aligned: 89
Modelled: 100
Confidence: 95.3%
Identity: 18%
PDB header:hydrolase
Chain: B: PDB Molecule:toxic extracellular endopeptidase;
PDBTitle: asap1 inactive mutant e294a, an extracellular toxic zinc2 metalloendopeptidase

Phyre2

PDB 1ex0 chain A domain 2

3D model

Region: 655 - 729
Aligned: 74
Modelled: 75
Confidence: 94.4%
Identity: 12%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: Transglutaminase, two C-terminal domains
Family: Transglutaminase, two C-terminal domains

Phyre2
1
c3ac0B_
2
c2x41A_
3
c3f93D_
4
c1ex1A_
5
c3bmxB_
6
c3lk6A_
7
c3sqlB_
8
d1x38a1
9
c3tevA_
10
d1tr9a_
11
d1x38a2
12
c2kl6A_
13
d1w8oa1
14
c2l0dA_
15
c2kutA_
16
d2vzsa2
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c1l9mB_
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d2q3za2
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c2x3bB_
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d1ex0a2
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3ac0B_
100.0 33 PDB header:hydrolase
Chain: B: PDB Molecule:beta-glucosidase i;
PDBTitle: crystal structure of beta-glucosidase from kluyveromyces marxianus in2 complex with glucose
2c2x41A_
100.0 30 PDB header:hydrolase
Chain: A: PDB Molecule:beta-glucosidase;
PDBTitle: structure of beta-glucosidase 3b from thermotoga neapolitana2 in complex with glucose
3c3f93D_
100.0 27 PDB header:hydrolase
Chain: D: PDB Molecule:beta-glucosidase;
PDBTitle: crystal structure of exo-1,3/1,4-beta-glucanase (exop) from2 pseudoalteromonas sp. bb1
4c1ex1A_
100.0 33 PDB header:hydrolase
Chain: A: PDB Molecule:protein (beta-d-glucan exohydrolase isoenzyme exo1);
PDBTitle: beta-d-glucan exohydrolase from barley
5c3bmxB_
100.0 25 PDB header:hydrolase
Chain: B: PDB Molecule:uncharacterized lipoprotein ybbd;
PDBTitle: beta-n-hexosaminidase (ybbd) from bacillus subtilis
6c3lk6A_
100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:lipoprotein ybbd;
PDBTitle: beta-n-hexosaminidase n318d mutant (ybbd_n318d) from bacillus subtilis
7c3sqlB_
100.0 20 PDB header:hydrolase
Chain: B: PDB Molecule:glycosyl hydrolase family 3;
PDBTitle: crystal structure of glycoside hydrolase from synechococcus
8d1x38a1
100.0 32 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:NagZ-like
9c3tevA_
100.0 19 PDB header:hydrolase
Chain: A: PDB Molecule:glycosyl hyrolase, family 3;
PDBTitle: the crystal structure of glycosyl hydrolase from deinococcus2 radiodurans r1
10d1tr9a_
100.0 22 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:NagZ-like
11d1x38a2
100.0 35 Fold:Flavodoxin-like
Superfamily:Beta-D-glucan exohydrolase, C-terminal domain
Family:Beta-D-glucan exohydrolase, C-terminal domain
12c2kl6A_
97.4 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution nmr structure of the cardb domain of pf1109 from2 pyrococcus furiosus. northeast structural genomics3 consortium target pfr193a
13d1w8oa1
97.3 19 Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:E-set domains of sugar-utilizing enzymes
14c2l0dA_
97.1 14 PDB header:cell adhesion
Chain: A: PDB Molecule:cell surface protein;
PDBTitle: solution nmr structure of putative cell surface protein ma_4588 (272-2 376 domain) from methanosarcina acetivorans, northeast structural3 genomics consortium target mvr254a
15c2kutA_
96.9 24 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution structure of gmr58a from geobacter metallireducens.2 northeast structural genomics consortium target gmr58a
16d2vzsa2
96.2 27 Fold:Immunoglobulin-like beta-sandwich
Superfamily:beta-Galactosidase/glucuronidase domain
Family:beta-Galactosidase/glucuronidase domain
17c1l9mB_
95.9 14 PDB header:transferase
Chain: B: PDB Molecule:protein-glutamine glutamyltransferase e3;
PDBTitle: three-dimensional structure of the human transglutaminase 32 enzyme: binding of calcium ions change structure for3 activation
18d2q3za2
95.8 16 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Transglutaminase, two C-terminal domains
Family:Transglutaminase, two C-terminal domains
19c2x3bB_
95.3 18 PDB header:hydrolase
Chain: B: PDB Molecule:toxic extracellular endopeptidase;
PDBTitle: asap1 inactive mutant e294a, an extracellular toxic zinc2 metalloendopeptidase
20d1ex0a2
94.4 12 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Transglutaminase, two C-terminal domains
Family:Transglutaminase, two C-terminal domains
21d1g0da2
not modelled 94.0 12 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Transglutaminase, two C-terminal domains
Family:Transglutaminase, two C-terminal domains
22c3isyA_
not modelled 93.5 22 PDB header:protein binding
Chain: A: PDB Molecule:intracellular proteinase inhibitor;
PDBTitle: crystal structure of an intracellular proteinase inhibitor (ipi,2 bsu11130) from bacillus subtilis at 2.61 a resolution
23d1vjja2
not modelled 93.2 14 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Transglutaminase, two C-terminal domains
Family:Transglutaminase, two C-terminal domains
24c3rgbA_
not modelled 90.6 24 PDB header:oxidoreductase
Chain: A: PDB Molecule:methane monooxygenase subunit b2;
PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath)
25d4ubpb_
not modelled 89.1 22 Fold:beta-clip
Superfamily:Urease, beta-subunit
Family:Urease, beta-subunit
26d2co7b1
not modelled 88.8 18 Fold:Immunoglobulin-like beta-sandwich
Superfamily:PapD-like
Family:Pilus chaperone
27c1yewI_
not modelled 88.7 25 PDB header:oxidoreductase, membrane protein
Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit;
PDBTitle: crystal structure of particulate methane monooxygenase
28c3fn9B_
not modelled 88.6 13 PDB header:hydrolase
Chain: B: PDB Molecule:putative beta-galactosidase;
PDBTitle: crystal structure of putative beta-galactosidase from bacteroides2 fragilis
29c2e6jA_
not modelled 87.8 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hydin protein;
PDBTitle: solution structure of the c-terminal papd-like domain from2 human hydin protein
30d1ejxb_
not modelled 87.6 24 Fold:beta-clip
Superfamily:Urease, beta-subunit
Family:Urease, beta-subunit
31d1e9ya1
not modelled 86.0 26 Fold:beta-clip
Superfamily:Urease, beta-subunit
Family:Urease, beta-subunit
32c2cqtA_
not modelled 86.0 17 PDB header:transferase
Chain: A: PDB Molecule:cellobiose phosphorylase;
PDBTitle: crystal structure of cellvibrio gilvus cellobiose phosphorylase2 crystallized from sodium/potassium phosphate
33c1kv3F_
not modelled 85.1 17 PDB header:transferase
Chain: F: PDB Molecule:protein-glutamine gamma-glutamyltransferase;
PDBTitle: human tissue transglutaminase in gdp bound form
34c3qgaD_
not modelled 84.4 20 PDB header:hydrolase
Chain: D: PDB Molecule:fusion of urease beta and gamma subunits;
PDBTitle: 3.0 a model of iron containing urease urea2b2 from helicobacter2 mustelae
35c1g0dA_
not modelled 83.7 13 PDB header:transferase
Chain: A: PDB Molecule:protein-glutamine gamma-glutamyltransferase;
PDBTitle: crystal structure of red sea bream transglutaminase
36c1f13A_
not modelled 83.5 12 PDB header:coagulation factor
Chain: A: PDB Molecule:cellular coagulation factor xiii zymogen;
PDBTitle: recombinant human cellular coagulation factor xiii
37d1v7wa2
not modelled 81.8 15 Fold:Supersandwich
Superfamily:Galactose mutarotase-like
Family:Glycosyltransferase family 36 N-terminal domain
38c1iq8B_
not modelled 80.6 9 PDB header:transferase
Chain: B: PDB Molecule:archaeosine trna-guanine transglycosylase;
PDBTitle: crystal structure of archaeosine trna-guanine2 transglycosylase from pyrococcus horikoshii
39d1jz8a1
not modelled 80.1 16 Fold:Immunoglobulin-like beta-sandwich
Superfamily:beta-Galactosidase/glucuronidase domain
Family:beta-Galactosidase/glucuronidase domain
40c1e9zA_
not modelled 80.0 26 PDB header:hydrolase
Chain: A: PDB Molecule:urease subunit alpha;
PDBTitle: crystal structure of helicobacter pylori urease
41c2a74B_
not modelled 79.5 14 PDB header:immune system
Chain: B: PDB Molecule:complement component c3c;
PDBTitle: human complement component c3c
42d2ccwa1
not modelled 78.9 18 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Plastocyanin/azurin-like
43c3rfrI_
not modelled 78.5 18 PDB header:oxidoreductase
Chain: I: PDB Molecule:pmob;
PDBTitle: crystal structure of particulate methane monooxygenase (pmmo) from2 methylocystis sp. strain m
44c3eoeC_
not modelled 77.8 17 PDB header:transferase
Chain: C: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pyruvate kinase from toxoplasma gondii, 55.m00007
45c3qisA_
not modelled 77.0 20 PDB header:hydrolase/protein binding
Chain: A: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1;
PDBTitle: recognition of the f&h motif by the lowe syndrome protein ocrl
46c2h47C_
not modelled 76.6 26 PDB header:oxidoreductase/electron transport
Chain: C: PDB Molecule:azurin;
PDBTitle: crystal structure of an electron transfer complex between2 aromatic amine dephydrogenase and azurin from alcaligenes3 faecalis (form 1)
47c3qbtH_
not modelled 75.5 15 PDB header:protein transport/hydrolase
Chain: H: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1;
PDBTitle: crystal structure of ocrl1 540-678 in complex with rab8a:gppnhp
48c2qsvA_
not modelled 75.2 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of protein of unknown function from porphyromonas2 gingivalis w83
49c1v7wA_
not modelled 74.9 17 PDB header:transferase
Chain: A: PDB Molecule:chitobiose phosphorylase;
PDBTitle: crystal structure of vibrio proteolyticus chitobiose phosphorylase in2 complex with glcnac
50c3hs0B_
not modelled 74.6 13 PDB header:immune system
Chain: B: PDB Molecule:cobra venom factor;
PDBTitle: cobra venom factor (cvf) in complex with human factor b
51d2g50a2
not modelled 74.4 18 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
52c5mdhB_
not modelled 73.2 24 PDB header:oxidoreductase
Chain: B: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of ternary complex of porcine cytoplasmic malate2 dehydrogenase alpha-ketomalonate and tnad at 2.4 angstroms resolution
53d1azca_
not modelled 72.9 18 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Plastocyanin/azurin-like
54d1civa1
not modelled 72.8 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
55d7mdha1
not modelled 72.5 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
56d1liua2
not modelled 72.3 19 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
57c2co7B_
not modelled 72.1 18 PDB header:fibril protein
Chain: B: PDB Molecule:putative fimbriae assembly chaperone;
PDBTitle: salmonella enterica safa pilin in complex with the safb2 chaperone (type ii)
58c3g6jB_
not modelled 71.9 15 PDB header:immune system
Chain: B: PDB Molecule:complement c3 alpha chain;
PDBTitle: c3b in complex with a c3b specific fab
59c1mldA_
not modelled 71.7 21 PDB header:oxidoreductase(nad(a)-choh(d))
Chain: A: PDB Molecule:malate dehydrogenase;
PDBTitle: refined structure of mitochondrial malate dehydrogenase2 from porcine heart and the consensus structure for3 dicarboxylic acid oxidoreductases
60d1y7ta1
not modelled 71.6 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
61d5mdha1
not modelled 71.5 24 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
62c1b8vA_
not modelled 71.0 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:protein (malate dehydrogenase);
PDBTitle: malate dehydrogenase from aquaspirillum arcticum
63c3fcsA_
not modelled 69.7 15 PDB header:cell adhesion/blood clotting
Chain: A: PDB Molecule:integrin, alpha 2b;
PDBTitle: structure of complete ectodomain of integrin aiibb3
64d1b8pa1
not modelled 69.1 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
65c3t07D_
not modelled 68.8 23 PDB header:transferase/transferase inhibitor
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of s. aureus pyruvate kinase in complex with a2 naturally occurring bis-indole alkaloid
66c1e0tD_
not modelled 68.6 14 PDB header:phosphotransferase
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: r292d mutant of e. coli pyruvate kinase
67c2ys4A_
not modelled 68.3 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hydrocephalus-inducing protein homolog;
PDBTitle: solution structure of the n-terminal papd-like domain of2 hydin protein from human
68c2a73B_
not modelled 67.8 14 PDB header:immune system
Chain: B: PDB Molecule:complement c3;
PDBTitle: human complement component c3
69c7mdhA_
not modelled 66.6 21 PDB header:chloroplastic malate dehydrogenase
Chain: A: PDB Molecule:protein (malate dehydrogenase);
PDBTitle: structural basis for light acitvation of a chloroplast enzyme. the2 structure of sorghum nadp-malate dehydrogenase in its oxidized form
70d1cc3a_
not modelled 66.5 16 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Plastocyanin/azurin-like
71c1sevA_
not modelled 66.4 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:malate dehydrogenase, glyoxysomal precursor;
PDBTitle: mature and translocatable forms of glyoxysomal malate2 dehydrogenase have different activities and stabilities3 but similar crystal structures
72c1smkD_
not modelled 66.4 12 PDB header:oxidoreductase
Chain: D: PDB Molecule:malate dehydrogenase, glyoxysomal;
PDBTitle: mature and translocatable forms of glyoxysomal malate2 dehydrogenase have different activities and stabilities3 but similar crystal structures
73d1cuoa_
not modelled 66.1 20 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Plastocyanin/azurin-like
74d1llda1
not modelled 65.7 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
75c2rdo7_
not modelled 65.5 15 PDB header:ribosome
Chain: 7: PDB Molecule:elongation factor g;
PDBTitle: 50s subunit with ef-g(gdpnp) and rrf bound
76d1ldma1
not modelled 64.3 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
77d1o6za1
not modelled 64.1 21 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
78d1e0ta2
not modelled 64.0 14 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
79d1nbca_
not modelled 63.3 18 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
80d1a5za1
not modelled 62.6 15 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
81d1llaa3
not modelled 61.7 16 Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:Arthropod hemocyanin, C-terminal domain
82c2b39B_
not modelled 61.7 14 PDB header:immune system
Chain: B: PDB Molecule:c3;
PDBTitle: structure of mammalian c3 with an intact thioester at 3a resolution
83c1wziA_
not modelled 60.9 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:malate dehydrogenase;
PDBTitle: structural basis for alteration of cofactor specificity of2 malate dehydrogenase from thermus flavus
84c1ogoX_
not modelled 60.6 18 PDB header:hydrolase
Chain: X: PDB Molecule:dextranase;
PDBTitle: dex49a from penicillium minioluteum complex with isomaltose
85c2dfdD_
not modelled 60.5 21 PDB header:oxidoreductase
Chain: D: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of human malate dehydrogenase type 2
86c3cu7A_
not modelled 60.1 13 PDB header:immune system
Chain: A: PDB Molecule:complement c5;
PDBTitle: human complement component 5
87d2ldxa1
not modelled 59.5 12 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
88c2pwzG_
not modelled 59.2 18 PDB header:oxidoreductase
Chain: G: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of the apo form of e.coli malate dehydrogenase
89d1i0za1
not modelled 58.7 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
90c2pn5A_
not modelled 58.5 17 PDB header:immune system
Chain: A: PDB Molecule:thioester-containing protein i;
PDBTitle: crystal structure of tep1r
91c8ldhA_
not modelled 58.5 19 PDB header:oxidoreductase(choh(d)-nad(a))
Chain: A: PDB Molecule:m4 apo-lactate dehydrogenase;
PDBTitle: refined crystal structure of dogfish m4 apo-lactate2 dehydrogenase
92c1hyhA_
not modelled 58.2 20 PDB header:oxidoreductase (choh(d)-nad+(a))
Chain: A: PDB Molecule:l-2-hydroxyisocaproate dehydrogenase;
PDBTitle: crystal structure of l-2-hydroxyisocaproate dehydrogenase from2 lactobacillus confusus at 2.2 angstroms resolution-an example of3 strong asymmetry between subunits
93d1jv2a2
not modelled 56.9 22 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Integrin domains
Family:Integrin domains
94d1p5va1
not modelled 55.8 17 Fold:Immunoglobulin-like beta-sandwich
Superfamily:PapD-like
Family:Pilus chaperone
95c2qv2A_
not modelled 55.7 24 PDB header:hydrolase
Chain: A: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1;
PDBTitle: a role of the lowe syndrome protein ocrl in early steps of2 the endocytic pathway
96c1jz6C_
not modelled 55.1 16 PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: e. coli (lacz) beta-galactosidase in complex with galacto-2 tetrazole
97c3tl2A_
not modelled 54.7 21 PDB header:oxidoreductase
Chain: A: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of bacillus anthracis str. ames malate dehydrogenase2 in closed conformation.
98d5ldha1
not modelled 54.7 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
99d1nwpa_
not modelled 53.8 21 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Plastocyanin/azurin-like
100c2hjrK_
not modelled 53.2 18 PDB header:oxidoreductase
Chain: K: PDB Molecule:malate dehydrogenase;
PDBTitle: crystal structure of cryptosporidium parvum malate2 dehydrogenase
101d1l4ia1
not modelled 53.1 15 Fold:Immunoglobulin-like beta-sandwich
Superfamily:PapD-like
Family:Pilus chaperone
102c2o14A_
not modelled 52.6 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein yxim;
PDBTitle: x-ray crystal structure of protein yxim_bacsu from bacillus2 subtilis. northeast structural genomics consortium target3 sr595
103c2l8aA_
not modelled 52.6 15 PDB header:hydrolase
Chain: A: PDB Molecule:endoglucanase;
PDBTitle: structure of a novel cbm3 lacking the calcium-binding site
104d1i10a1
not modelled 52.5 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
105c2v6bB_
not modelled 52.0 27 PDB header:oxidoreductase
Chain: B: PDB Molecule:l-lactate dehydrogenase;
PDBTitle: crystal structure of lactate dehydrogenase from deinococcus2 radiodurans (apo form)
106c2jtxA_
not modelled 51.9 55 PDB header:transcription
Chain: A: PDB Molecule:transcription initiation factor iie subunit
PDBTitle: nmr structure of the tfiie-alpha carboxyl terminus
107c1lldA_
not modelled 51.2 14 PDB header:oxidoreductase(choh (d)-nad (a))
Chain: A: PDB Molecule:l-lactate dehydrogenase;
PDBTitle: molecular basis of allosteric activation of bacterial l-lactate2 dehydrogenase
108c3mpbA_
not modelled 51.1 21 PDB header:isomerase
Chain: A: PDB Molecule:sugar isomerase;
PDBTitle: z5688 from e. coli o157:h7 bound to fructose
109d1a3xa2
not modelled 50.3 22 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
110d9ldta1
not modelled 50.1 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
111c2rnqA_
not modelled 49.5 55 PDB header:transcription
Chain: A: PDB Molecule:transcription initiation factor iie subunit
PDBTitle: solution structure of the c-terminal acidic domain of tfiie2 alpha
112c1a5zA_
not modelled 49.2 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-lactate dehydrogenase;
PDBTitle: lactate dehydrogenase from thermotoga maritima (tmldh)
113d1hyha1
not modelled 48.8 20 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:LDH N-terminal domain-like
114c1t5aB_
not modelled 48.7 17 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase, m2 isozyme;
PDBTitle: human pyruvate kinase m2
115c3q48B_
not modelled 48.6 13 PDB header:chaperone
Chain: B: PDB Molecule:chaperone cupb2;
PDBTitle: crystal structure of pseudomonas aeruginosa cupb2 chaperone
116c1z9sA_
not modelled 47.9 16 PDB header:chaperone/immune system
Chain: A: PDB Molecule:chaperone protein caf1m;
PDBTitle: crystal structure of the native chaperone:subunit:subunit2 caf1m:caf1:caf1 complex
117d1iq8a1
not modelled 47.5 8 Fold:TIM beta/alpha-barrel
Superfamily:tRNA-guanine transglycosylase
Family:tRNA-guanine transglycosylase
118c3p7mC_
not modelled 47.2 15 PDB header:oxidoreductase
Chain: C: PDB Molecule:malate dehydrogenase;
PDBTitle: structure of putative lactate dehydrogenase from francisella2 tularensis subsp. tularensis schu s4
119d1joia_
not modelled 47.1 18 Fold:Cupredoxin-like
Superfamily:Cupredoxins
Family:Plastocyanin/azurin-like
120c2e28A_
not modelled 46.9 19 PDB header:transferase
Chain: A: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure analysis of pyruvate kinase from bacillus2 stearothermophilus

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