Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP37652
DateThu Jan 5 11:56:24 GMT 2012
Unique Job ID1aebc5f4b89062a4

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1yq2a3
Top template information
Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:beta-Galactosidase/glucuronidase, N-terminal domain
Confidence and coverage
Confidence: 96.6% Coverage: 12%
93 residues ( 12% of your sequence) have been modelled with 96.6% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
282 residues ( 36%) 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  MKRKLFWICAVAMGMSAFPSFMTQATPATQPLINAEPAVAAQTEQNPQVGQVMPGVQGAD
Secondary structure 
SS confidence 
Disorder  ????
???????????????????????????????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  APVVAQNGPSRDVKLTFAQIAPPPGSMVLRGINPNGSIEFGMRSDEVVTKAMLNLEYTPS
Secondary structure 
SS confidence 
Disorder  ????????????
?????
???
?
?
?
??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  PSLLPVQSQLKVYLNDELMGVLPVTKEQLGKKTLAQMPINPLFISDFNRVRLEFVGHYQD
Secondary structure 
SS confidence 
Disorder  ????????
?????????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  VCEKPASTTLWLDVGRSSGLDLTYQTLNVKNDLSHFPVPFFDPSDNRTNTLPMVFAGAPD
Secondary structure 
SS confidence 
Disorder 
??????
???
??
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  VGLQQASAIVASWFGSRSGWRGQNFPVLYNQLPDRNAIVFATNDKRPDFLRDHPAVKAPV
Secondary structure 
SS confidence 
Disorder 
???
?
?
?????
????????
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  IEMINHPQNPYVKLLVVFGRDDKDLLQAAKGIAQGNILFRGESVVVNEVKPLLPRKPYDA
Secondary structure 
SS confidence 
Disorder 
????????????
????????????
??
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  PNWVRTDRPVTFGELKTYEEQLQSSGLEPAAINVSLNLPPDLYLMRSTGIDMDINYRYTM
Secondary structure 
SS confidence 
Disorder  ?
????
?
??????
?
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  PPVKDSSRMDISLNNQFLQSFNLSSKQEANRLLLRIPVLQGLLDGKTDVSIPALKLGATN
Secondary structure 
SS confidence 
Disorder  ??????
?
????????
?????????
??
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  QLRFDFEYMNPMPGGSVDNCITFQPVQNHVVIGDDSTIDFSKYYHFIPMPDLRAFANAGF
Secondary structure 
SS confidence 
Disorder 
?
??????
?
?
???
???
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  PFSRMADLSQTITVMPKAPNEAQMETLLNTVGFIGAQTGFPAINLTVTDDGSTIQGKDAD
Secondary structure 
SS confidence 
Disorder 
?
?????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  IMIIGGIPDKLKDDKQIDLLVQATESWVKTPMRQTPFPGIVPDESDRAAETRSTLTSSGA
Secondary structure 
SS confidence 
Disorder 
????????????
???????????????????????????????????
???
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  MAAVIGFQSPYNDQRSVIALLADSPRGYEMLNDAVNDSGKRATMFGSVAVIRESGINSLR
Secondary structure 
SS confidence 
Disorder  ?
?????
?
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........
Sequence  VGDVYYVGHLPWFERVWYALANHPILLAVLAAISVILLAWVLWRLLRIISRRRLNPDNE
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 1yq2 chain A domain 3

3D model

Region: 99 - 203
Aligned: 93
Modelled: 97
Confidence: 96.6%
Identity: 17%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: beta-Galactosidase/glucuronidase, N-terminal domain

Phyre2

PDB 1nkg chain A domain 2

3D model

Region: 91 - 176
Aligned: 81
Modelled: 86
Confidence: 96.2%
Identity: 17%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: Rhamnogalacturonase B, RhgB, C-terminal domain

Phyre2

PDB 1yq2 chain C

3D model

Region: 99 - 203
Aligned: 93
Modelled: 105
Confidence: 94.4%
Identity: 17%
PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: beta-galactosidase from arthrobacter sp. c2-2 (isoenzyme c2-2 2-1)

Phyre2

PDB 3bga chain B

3D model

Region: 99 - 203
Aligned: 91
Modelled: 105
Confidence: 94.2%
Identity: 24%
PDB header:hydrolase
Chain: B: PDB Molecule:beta-galactosidase;
PDBTitle: crystal structure of beta-galactosidase from bacteroides2 thetaiotaomicron vpi-5482

Phyre2

PDB 3mv1 chain 4

3D model

Region: 99 - 186
Aligned: 74
Modelled: 88
Confidence: 94.2%
Identity: 11%
PDB header:hydrolase
Chain: 4: PDB Molecule:beta-galactosidase;
PDBTitle: e.coli (lacz) beta-galactosidase (r599a) in complex with guanidinium

Phyre2

PDB 2w3j chain A

3D model

Region: 392 - 486
Aligned: 72
Modelled: 81
Confidence: 92.7%
Identity: 14%
PDB header:sugar-binding protein
Chain: A: PDB Molecule:carbohydrate binding module;
PDBTitle: structure of a family 35 carbohydrate binding module from2 an environmental isolate

Phyre2

PDB 1jz8 chain A domain 3

3D model

Region: 128 - 203
Aligned: 70
Modelled: 76
Confidence: 92.0%
Identity: 11%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: beta-Galactosidase/glucuronidase, N-terminal domain

Phyre2

PDB 2je8 chain A domain 4

3D model

Region: 131 - 176
Aligned: 40
Modelled: 46
Confidence: 91.8%
Identity: 20%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: beta-Galactosidase/glucuronidase, N-terminal domain

Phyre2

PDB 1l8n chain A domain 2

3D model

Region: 224 - 332
Aligned: 101
Modelled: 109
Confidence: 91.6%
Identity: 16%
Fold: Zincin-like
Superfamily: beta-N-acetylhexosaminidase-like domain
Family: alpha-D-glucuronidase, N-terminal domain

Phyre2

PDB 2vzs chain A domain 4

3D model

Region: 131 - 183
Aligned: 50
Modelled: 50
Confidence: 91.3%
Identity: 14%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: beta-Galactosidase/glucuronidase, N-terminal domain

Phyre2

PDB 1jz6 chain C

3D model

Region: 99 - 203
Aligned: 91
Modelled: 105
Confidence: 90.8%
Identity: 10%
PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: e. coli (lacz) beta-galactosidase in complex with galacto-2 tetrazole

Phyre2

PDB 2okx chain B

3D model

Region: 99 - 206
Aligned: 97
Modelled: 108
Confidence: 89.2%
Identity: 15%
PDB header:hydrolase
Chain: B: PDB Molecule:rhamnosidase b;
PDBTitle: crystal structure of gh78 family rhamnosidase of bacillus sp. gl1 at2 1.9 a

Phyre2

PDB 2vzv chain B

3D model

Region: 131 - 200
Aligned: 67
Modelled: 67
Confidence: 88.7%
Identity: 12%
PDB header:hydrolase
Chain: B: PDB Molecule:exo-beta-d-glucosaminidase;
PDBTitle: substrate complex of amycolatopsis orientalis exo-2 chitosanase csxa e541a with chitosan

Phyre2

PDB 2wz8 chain A

3D model

Region: 401 - 485
Aligned: 71
Modelled: 71
Confidence: 88.6%
Identity: 15%
PDB header:sugar binding protein
Chain: A: PDB Molecule:cellulosome protein dockerin type i;
PDBTitle: family 35 carbohydrate binding module from clostridium2 thermocellum

Phyre2

PDB 2je8 chain B

3D model

Region: 131 - 174
Aligned: 38
Modelled: 44
Confidence: 87.4%
Identity: 21%
PDB header:hydrolase
Chain: B: PDB Molecule:beta-mannosidase;
PDBTitle: structure of a beta-mannosidase from bacteroides2 thetaiotaomicron

Phyre2

PDB 1nkg chain A

3D model

Region: 89 - 181
Aligned: 88
Modelled: 93
Confidence: 87.1%
Identity: 15%
PDB header:lyase
Chain: A: PDB Molecule:rhamnogalacturonase b;
PDBTitle: rhamnogalacturonan lyase from aspergillus aculeatus

Phyre2

PDB 1bhg chain A domain 2

3D model

Region: 99 - 191
Aligned: 81
Modelled: 93
Confidence: 85.8%
Identity: 16%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: beta-Galactosidase/glucuronidase, N-terminal domain

Phyre2

PDB 1uxx chain X

3D model

Region: 413 - 486
Aligned: 59
Modelled: 60
Confidence: 85.5%
Identity: 12%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: Family 6 carbohydrate binding module, CBM6

Phyre2

PDB 1uxz chain A

3D model

Region: 411 - 487
Aligned: 63
Modelled: 63
Confidence: 85.0%
Identity: 10%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: Family 6 carbohydrate binding module, CBM6

Phyre2

PDB 3gm8 chain A

3D model

Region: 99 - 191
Aligned: 79
Modelled: 93
Confidence: 84.4%
Identity: 15%
PDB header:hydrolase
Chain: A: PDB Molecule:glycoside hydrolase family 2, candidate beta-glycosidase;
PDBTitle: crystal structure of a beta-glycosidase from bacteroides vulgatus

Phyre2

PDB 1w9s chain A

3D model

Region: 69 - 194
Aligned: 116
Modelled: 116
Confidence: 64.1%
Identity: 12%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: Family 6 carbohydrate binding module, CBM6

Phyre2
1
d1yq2a3
2
d1nkga2
3
c1yq2C_
4
c3bgaB_
5
c3mv14_
6
c2w3jA_
7
d1jz8a3
8
d2je8a4
9
d1l8na2
10
d2vzsa4
11
c1jz6C_
12
c2okxB_
13
c2vzvB_
14
c2wz8A_
15
c2je8B_
16
c1nkgA_
17
d1bhga2
18
d1uxxx_
19
d1uxza_
20
c3gm8A_
21
22
23
24
25
26
27
28
29
30
31
32
33
d1w9sa_
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
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71
72
73
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75
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99



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1yq2a3
96.6 17 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:beta-Galactosidase/glucuronidase, N-terminal domain
2d1nkga2
96.2 17 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Rhamnogalacturonase B, RhgB, C-terminal domain
3c1yq2C_
94.4 17 PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: beta-galactosidase from arthrobacter sp. c2-2 (isoenzyme c2-2 2-1)
4c3bgaB_
94.2 24 PDB header:hydrolase
Chain: B: PDB Molecule:beta-galactosidase;
PDBTitle: crystal structure of beta-galactosidase from bacteroides2 thetaiotaomicron vpi-5482
5c3mv14_
94.2 11 PDB header:hydrolase
Chain: 4: PDB Molecule:beta-galactosidase;
PDBTitle: e.coli (lacz) beta-galactosidase (r599a) in complex with guanidinium
6c2w3jA_
92.7 14 PDB header:sugar-binding protein
Chain: A: PDB Molecule:carbohydrate binding module;
PDBTitle: structure of a family 35 carbohydrate binding module from2 an environmental isolate
7d1jz8a3
92.0 11 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:beta-Galactosidase/glucuronidase, N-terminal domain
8d2je8a4
91.8 20 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:beta-Galactosidase/glucuronidase, N-terminal domain
9d1l8na2
91.6 16 Fold:Zincin-like
Superfamily:beta-N-acetylhexosaminidase-like domain
Family:alpha-D-glucuronidase, N-terminal domain
10d2vzsa4
91.3 14 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:beta-Galactosidase/glucuronidase, N-terminal domain
11c1jz6C_
90.8 10 PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: e. coli (lacz) beta-galactosidase in complex with galacto-2 tetrazole
12c2okxB_
89.2 15 PDB header:hydrolase
Chain: B: PDB Molecule:rhamnosidase b;
PDBTitle: crystal structure of gh78 family rhamnosidase of bacillus sp. gl1 at2 1.9 a
13c2vzvB_
88.7 12 PDB header:hydrolase
Chain: B: PDB Molecule:exo-beta-d-glucosaminidase;
PDBTitle: substrate complex of amycolatopsis orientalis exo-2 chitosanase csxa e541a with chitosan
14c2wz8A_
88.6 15 PDB header:sugar binding protein
Chain: A: PDB Molecule:cellulosome protein dockerin type i;
PDBTitle: family 35 carbohydrate binding module from clostridium2 thermocellum
15c2je8B_
87.4 21 PDB header:hydrolase
Chain: B: PDB Molecule:beta-mannosidase;
PDBTitle: structure of a beta-mannosidase from bacteroides2 thetaiotaomicron
16c1nkgA_
87.1 15 PDB header:lyase
Chain: A: PDB Molecule:rhamnogalacturonase b;
PDBTitle: rhamnogalacturonan lyase from aspergillus aculeatus
17d1bhga2
85.8 16 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:beta-Galactosidase/glucuronidase, N-terminal domain
18d1uxxx_
85.5 12 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 6 carbohydrate binding module, CBM6
19d1uxza_
85.0 10 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 6 carbohydrate binding module, CBM6
20c3gm8A_
84.4 15 PDB header:hydrolase
Chain: A: PDB Molecule:glycoside hydrolase family 2, candidate beta-glycosidase;
PDBTitle: crystal structure of a beta-glycosidase from bacteroides vulgatus
21c3obaA_
not modelled 79.7 16 PDB header:hydrolase
Chain: A: PDB Molecule:beta-galactosidase;
PDBTitle: structure of the beta-galactosidase from kluyveromyces lactis
22c3cmgA_
not modelled 78.5 15 PDB header:hydrolase
Chain: A: PDB Molecule:putative beta-galactosidase;
PDBTitle: crystal structure of putative beta-galactosidase from bacteroides2 fragilis
23c3lpgA_
not modelled 74.4 18 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:beta-glucuronidase;
PDBTitle: structure of e. coli beta-glucuronidase bound with a novel, potent2 inhibitor 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-((6-methyl-2-oxo-1,3 2-dihydroquinolin-3-yl)methyl)urea
24c2vzqA_
not modelled 72.1 17 PDB header:hydrolase
Chain: A: PDB Molecule:exo-beta-d-glucosaminidase;
PDBTitle: c-terminal cbm35 from amycolatopsis orientalis exo-2 chitosanase csxa in complex with digalacturonic acid
25d1uy4a_
not modelled 72.0 15 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 6 carbohydrate binding module, CBM6
26c2v4vA_
not modelled 71.9 10 PDB header:hydrolase
Chain: A: PDB Molecule:gh59 galactosidase;
PDBTitle: crystal structure of a family 6 carbohydrate-binding module2 from clostridium cellulolyticum in complex with xylose
27c1bhgB_
not modelled 71.5 15 PDB header:glycosidase
Chain: B: PDB Molecule:beta-glucuronidase;
PDBTitle: human beta-glucuronidase at 2.6 a resolution
28d1od3a_
not modelled 70.8 16 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 6 carbohydrate binding module, CBM6
29c2w1wB_
not modelled 70.6 21 PDB header:hydrolase
Chain: B: PDB Molecule:lipolytic enzyme, g-d-s-l;
PDBTitle: native structure of a family 35 carbohydrate binding module2 from clostridium thermocellum
30c2w87B_
not modelled 68.4 10 PDB header:hydrolase
Chain: B: PDB Molecule:esterase d;
PDBTitle: xyl-cbm35 in complex with glucuronic acid containing2 disaccharide.
31d1h41a2
not modelled 68.3 12 Fold:Zincin-like
Superfamily:beta-N-acetylhexosaminidase-like domain
Family:alpha-D-glucuronidase, N-terminal domain
32c3fn9B_
not modelled 66.8 16 PDB header:hydrolase
Chain: B: PDB Molecule:putative beta-galactosidase;
PDBTitle: crystal structure of putative beta-galactosidase from bacteroides2 fragilis
33d1w9sa_
64.1 12 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 6 carbohydrate binding module, CBM6
34c1naeA_
not modelled 57.7 16 PDB header:hydrolase
Chain: A: PDB Molecule:putative xylanase;
PDBTitle: structure of cscbm6-3 from clostridium stercorarium in2 complex with xylotriose
35d1tg7a2
not modelled 56.7 9 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Beta-galactosidase LacA, domains 4 and 5
36d1tg7a3
not modelled 50.4 16 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Beta-galactosidase LacA, domains 4 and 5
37c3ohnA_
not modelled 49.8 7 PDB header:membrane protein
Chain: A: PDB Molecule:outer membrane usher protein fimd;
PDBTitle: crystal structure of the fimd translocation domain
38c2vqiA_
not modelled 44.6 11 PDB header:transport
Chain: A: PDB Molecule:outer membrane usher protein papc;
PDBTitle: structure of the p pilus usher (papc) translocation pore
39c2y8kA_
not modelled 43.4 18 PDB header:hydrolase
Chain: A: PDB Molecule:carbohydrate binding family 6;
PDBTitle: structure of ctgh5-cbm6, an arabinoxylan-specific xylanase.
40c2kluA_
not modelled 40.9 15 PDB header:immune system, membrane protein
Chain: A: PDB Molecule:t-cell surface glycoprotein cd4;
PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4
41d1zzka1
not modelled 39.2 10 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
42c2kncA_
not modelled 37.3 17 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
43c2bgpA_
not modelled 37.1 15 PDB header:carbohydrate binding protein
Chain: A: PDB Molecule:endo-b1,4-mannanase 5c;
PDBTitle: mannan binding module from man5c in bound conformation
44c3hfxA_
not modelled 35.4 13 PDB header:transport protein
Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter;
PDBTitle: crystal structure of carnitine transporter
45d1wvna1
not modelled 32.7 12 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
46d3dtub2
not modelled 27.3 23 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
47c3j0cH_
not modelled 27.1 14 PDB header:virus
Chain: H: PDB Molecule:e2 envelope glycoprotein;
PDBTitle: models of e1, e2 and cp of venezuelan equine encephalitis virus tc-832 strain restrained by a near atomic resolution cryo-em map
48c2kppA_
not modelled 26.8 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin0431 protein;
PDBTitle: solution nmr structure of lin0431 protein from listeria innocua.2 northeast structural genomics consortium target lkr112
49c2kklA_
not modelled 26.2 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein mb1858;
PDBTitle: solution nmr structure of fha domain of mb1858 from2 mycobacterium bovis. northeast structural genomics3 consortium target mbr243c (24-155).
50c3fwlA_
not modelled 25.0 13 PDB header:transferase, hydrolase
Chain: A: PDB Molecule:penicillin-binding protein 1b;
PDBTitle: crystal structure of the full-length transglycosylase pbp1b2 from escherichia coli
51c3c7hA_
not modelled 24.9 12 PDB header:hydrolase
Chain: A: PDB Molecule:endo-1,4-beta-xylanase;
PDBTitle: crystal structure of glycoside hydrolase family 43 arabinoxylan2 arabinofuranohydrolase from bacillus subtilis in complex with axos-4-3 0.5.
52c2kncB_
not modelled 24.8 30 PDB header:cell adhesion
Chain: B: PDB Molecule:integrin beta-3;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
53c2w8aC_
not modelled 22.5 13 PDB header:membrane protein
Chain: C: PDB Molecule:glycine betaine transporter betp;
PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate
54c3oggA_
not modelled 21.3 13 PDB header:toxin
Chain: A: PDB Molecule:botulinum neurotoxin type d;
PDBTitle: crystal structure of the receptor binding domain of botulinum2 neurotoxin d
55d3ehbb2
not modelled 19.7 17 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
56c2rmzA_
not modelled 19.4 30 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin beta-3;
PDBTitle: bicelle-embedded integrin beta3 transmembrane segment
57c1mqrA_
not modelled 19.3 12 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-d-glucuronidase;
PDBTitle: the crystal structure of alpha-d-glucuronidase (e386q) from bacillus2 stearothermophilus t-6
58c1m57H_
not modelled 18.9 23 PDB header:oxidoreductase
Chain: H: PDB Molecule:cytochrome c oxidase;
PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant))
59c2cdpC_
not modelled 18.6 10 PDB header:hydrolase
Chain: C: PDB Molecule:beta-agarase 1;
PDBTitle: structure of a cbm6 in complex with neoagarohexaose
60d3bwud1
not modelled 17.0 15 Fold:FimD N-terminal domain-like
Superfamily:FimD N-terminal domain-like
Family:Usher N-domain
61c1v8cA_
not modelled 16.7 20 PDB header:protein binding
Chain: A: PDB Molecule:moad related protein;
PDBTitle: crystal structure of moad related protein from thermus2 thermophilus hb8
62c2l0dA_
not modelled 16.5 8 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
63d1tf4a2
not modelled 15.2 7 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily:Carbohydrate-binding domain
Family:Cellulose-binding domain family III
64d1j4wa1
not modelled 15.0 14 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
65d1khma_
not modelled 14.1 10 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
66d1fftb2
not modelled 13.3 0 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
67c1qleB_
not modelled 13.0 17 PDB header:oxidoreductase/immune system
Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii;
PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment
68c1ar1B_
not modelled 13.0 17 PDB header:complex (oxidoreductase/antibody)
Chain: B: PDB Molecule:cytochrome c oxidase;
PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment
69c3poaA_
not modelled 12.7 11 PDB header:peptide binding protein
Chain: A: PDB Molecule:putative uncharacterized protein tb39.8;
PDBTitle: structural and functional analysis of phosphothreonine-dependent fha2 domain interactions
70c2jwaA_
not modelled 12.4 25 PDB header:transferase
Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2;
PDBTitle: erbb2 transmembrane segment dimer spatial structure
71d1isia_
not modelled 12.4 25 Fold:Flavodoxin-like
Superfamily:N-(deoxy)ribosyltransferase-like
Family:ADP ribosyl cyclase-like
72c3rfzB_
not modelled 11.8 7 PDB header:cell adhesion/transport/chaperone
Chain: B: PDB Molecule:outer membrane usher protein, type 1 fimbrial synthesis;
PDBTitle: crystal structure of the fimd usher bound to its cognate fimc:fimh2 substrate
73c1xc6A_
not modelled 11.2 21 PDB header:hydrolase
Chain: A: PDB Molecule:beta-galactosidase;
PDBTitle: native structure of beta-galactosidase from penicillium sp. in complex2 with galactose
74d1zdxa1
not modelled 11.2 17 Fold:FimD N-terminal domain-like
Superfamily:FimD N-terminal domain-like
Family:Usher N-domain
75d1edqa1
not modelled 10.7 26 Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:E-set domains of sugar-utilizing enzymes
76c3fcgB_
not modelled 9.2 10 PDB header:membrane protein, protein transport
Chain: B: PDB Molecule:f1 capsule-anchoring protein;
PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher
77c2k1aA_
not modelled 9.0 16 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment
78c2w0cC_
not modelled 8.9 10 PDB header:virus
Chain: C: PDB Molecule:major capsid protein p2;
PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2
79d2vdfa1
not modelled 8.7 18 Fold:Transmembrane beta-barrels
Superfamily:OMPT-like
Family:Outer membrane adhesin/invasin OpcA
80c2l2tA_
not modelled 8.5 14 PDB header:membrane protein
Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4;
PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain
81d1yq2a1
not modelled 8.4 11 Fold:Immunoglobulin-like beta-sandwich
Superfamily:beta-Galactosidase/glucuronidase domain
Family:beta-Galactosidase/glucuronidase domain
82d2ef1a1
not modelled 8.2 23 Fold:Flavodoxin-like
Superfamily:N-(deoxy)ribosyltransferase-like
Family:ADP ribosyl cyclase-like
83c2eg9B_
not modelled 8.0 13 PDB header:hydrolase
Chain: B: PDB Molecule:adp-ribosyl cyclase 1;
PDBTitle: crystal structure of the truncated extracellular domain of2 mouse cd38
84c2uveA_
not modelled 7.9 13 PDB header:hydrolase
Chain: A: PDB Molecule:exopolygalacturonase;
PDBTitle: structure of yersinia enterocolitica family 282 exopolygalacturonase
85d1x4ma1
not modelled 7.8 20 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
86c2b2hA_
not modelled 7.6 13 PDB header:transport protein
Chain: A: PDB Molecule:ammonium transporter;
PDBTitle: ammonium transporter amt-1 from a. fulgidus (as)
87d1zdva1
not modelled 7.6 17 Fold:FimD N-terminal domain-like
Superfamily:FimD N-terminal domain-like
Family:Usher N-domain
88d1h7sa1
not modelled 7.4 10 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:DNA gyrase/MutL, second domain
89d3btaa1
not modelled 7.3 15 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Clostridium neurotoxins, the second last domain
90d1gmua2
not modelled 7.0 10 Fold:Ferredoxin-like
Superfamily:Urease metallochaperone UreE, C-terminal domain
Family:Urease metallochaperone UreE, C-terminal domain
91c2kfdA_
not modelled 7.0 38 PDB header:nuclear protein
Chain: A: PDB Molecule:pre-mrna-processing protein prp40;
PDBTitle: prp40 ff4 domain
92d2vmha1
not modelled 7.0 14 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:NPCBM-like
93c2kd2A_
not modelled 6.9 31 PDB header:apoptosis
Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1;
PDBTitle: nmr structure of faim-ctd
94d2obba1
not modelled 6.6 16 Fold:HAD-like
Superfamily:HAD-like
Family:BT0820-like
95c2jwpA_
not modelled 6.6 8 PDB header:sugar binding protein
Chain: A: PDB Molecule:malectin;
PDBTitle: malectin
96c2z64C_
not modelled 6.6 11 PDB header:immune system
Chain: C: PDB Molecule:lymphocyte antigen 96;
PDBTitle: crystal structure of mouse tlr4 and mouse md-2 complex
97c2xfgB_
not modelled 6.6 13 PDB header:hydrolase/sugar binding protein
Chain: B: PDB Molecule:endoglucanase 1;
PDBTitle: reassembly and co-crystallization of a family 9 processive2 endoglucanase from separately expressed gh9 and cbm3c3 modules
98c3qnqD_
not modelled 6.5 16 PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
99c2ifoA_
not modelled 6.3 14 PDB header:virus
Chain: A: PDB Molecule:inovirus;
PDBTitle: model-building studies of inovirus: genetic variations on a2 geometric theme

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