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2WVZ
Asym. Unit
Info
Asym.Unit (502 KB)
Biol.Unit 1 (131 KB)
Biol.Unit 2 (131 KB)
Biol.Unit 3 (129 KB)
Biol.Unit 4 (129 KB)
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(1)
Title
:
STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT3990 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482
Authors
:
M. D. L. Suits, Y. Zhu, A. Thompson, H. J. Gilbert, G. J. Davies
Date
:
21 Oct 09 (Deposition) - 29 Dec 09 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Hydrolase, Gh92, Bt3990, Glycoside Hydrolase Family 92
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhu, M. D. L. Suits, A. Thompson, S. Chavan, Z. Dinev, C. Dumon, N. Smith, K. W. Moremen, Y. Xiang, A. Siriwardena, S. J. Williams, H. J. Gilbert, G. J. Davies
Mechanistic Insights Into A Ca2+-Dependent Family Of A-Mannosidases In A Human Gut Symbiont.
Nat. Chem. Biol. V. 6 125 2010
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: KIFUNENSINE (KIFa)
3b: KIFUNENSINE (KIFb)
3c: KIFUNENSINE (KIFc)
3d: KIFUNENSINE (KIFd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
KIF
4
Ligand/Ion
KIFUNENSINE
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:601 , GLN A:602 , ASP A:644 , KIF A:801 , HOH A:2188 , HOH A:2209
BINDING SITE FOR RESIDUE CA A 800
02
AC2
SOFTWARE
SER A:86 , TRP A:88 , ILE A:89 , TRP A:347 , ASP A:348 , TRP A:385 , CYS A:393 , GLU A:533 , GLU A:585 , ASN A:601 , GLN A:602 , ASP A:644 , CA A:800 , HOH A:2210 , HOH A:2244
BINDING SITE FOR RESIDUE KIF A 801
03
AC3
SOFTWARE
GLU A:272
BINDING SITE FOR RESIDUE GOL A 802
04
AC4
SOFTWARE
ASN B:601 , GLN B:602 , ASP B:644 , KIF B:801 , HOH B:2136
BINDING SITE FOR RESIDUE CA B 800
05
AC5
SOFTWARE
SER B:86 , TRP B:88 , ASP B:348 , TRP B:385 , CYS B:393 , GLU B:533 , GLU B:585 , ASN B:601 , GLN B:602 , ASP B:644 , CA B:800 , HOH B:2179
BINDING SITE FOR RESIDUE KIF B 801
06
AC6
SOFTWARE
TYR B:126 , GLU B:272 , ALA B:275
BINDING SITE FOR RESIDUE GOL B 803
07
AC7
SOFTWARE
ASN C:601 , GLN C:602 , ASP C:644 , KIF C:801 , HOH C:2156
BINDING SITE FOR RESIDUE CA C 800
08
AC8
SOFTWARE
SER C:86 , TRP C:88 , TRP C:347 , ASP C:348 , TRP C:385 , MET C:394 , GLU C:533 , GLU C:585 , ASN C:601 , GLN C:602 , ASP C:644 , CA C:800 , HOH C:2137 , HOH C:2157
BINDING SITE FOR RESIDUE KIF C 801
09
AC9
SOFTWARE
ASN A:709 , GLY A:710 , ASP C:65 , TRP C:67 , HOH C:2203
BINDING SITE FOR RESIDUE GOL C 802
10
BC1
SOFTWARE
ASN D:601 , GLN D:602 , ASP D:644 , KIF D:801 , HOH D:2155 , HOH D:2166
BINDING SITE FOR RESIDUE CA D 800
11
BC2
SOFTWARE
SER D:86 , TRP D:88 , TRP D:347 , ASP D:348 , TRP D:385 , GLU D:533 , GLU D:585 , ASN D:601 , GLN D:602 , ASP D:644 , CA D:800 , HOH D:2166
BINDING SITE FOR RESIDUE KIF D 801
12
BC3
SOFTWARE
GLU D:272
BINDING SITE FOR RESIDUE GOL D 802
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_2wvzA02 (A:289-312,A:607-631,A:632-748)
1b: CATH_2wvzB02 (B:289-312,B:607-631,B:632-748)
1c: CATH_2wvzC02 (C:289-312,C:607-631,C:632-748)
1d: CATH_2wvzD02 (D:289-312,D:607-631,D:632-748)
2a: CATH_2wvzA03 (A:344-438)
2b: CATH_2wvzB03 (B:344-438)
2c: CATH_2wvzC03 (C:344-438)
2d: CATH_2wvzD03 (D:344-438)
3a: CATH_2wvzA01 (A:20-53,A:54-288,A:313-343)
3b: CATH_2wvzB01 (B:20-53,B:54-288,B:313-343)
3c: CATH_2wvzC01 (C:20-53,C:54-288,C:313-343)
3d: CATH_2wvzD01 (D:20-53,D:54-288,D:313-343)
View:
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Classes
(
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(
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GH92 mannosidase fold
(8)
Homologous Superfamily
:
GH92 mannosidase domain
(8)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
1a
2wvzA02
A:289-312,A:607-631,A:632-748
1b
2wvzB02
B:289-312,B:607-631,B:632-748
1c
2wvzC02
C:289-312,C:607-631,C:632-748
1d
2wvzD02
D:289-312,D:607-631,D:632-748
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
(267)
Homologous Superfamily
:
alpha-1,2-mannosidase
(8)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
2a
2wvzA03
A:344-438
2b
2wvzB03
B:344-438
2c
2wvzC03
C:344-438
2d
2wvzD03
D:344-438
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
[code=2.70.98.10, no name defined]
(116)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
3a
2wvzA01
A:20-53,A:54-288,A:313-343
3b
2wvzB01
B:20-53,B:54-288,B:313-343
3c
2wvzC01
C:20-53,C:54-288,C:313-343
3d
2wvzD01
D:20-53,D:54-288,D:313-343
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_92_2wvzD01 (D:228-737)
1b: PFAM_Glyco_hydro_92_2wvzD02 (D:228-737)
1c: PFAM_Glyco_hydro_92_2wvzD03 (D:228-737)
1d: PFAM_Glyco_hydro_92_2wvzD04 (D:228-737)
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)
Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_92
(7)
Bacteroides thetaiotaomicron
(7)
1a
Glyco_hydro_92-2wvzD01
D:228-737
1b
Glyco_hydro_92-2wvzD02
D:228-737
1c
Glyco_hydro_92-2wvzD03
D:228-737
1d
Glyco_hydro_92-2wvzD04
D:228-737
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Asym.Unit (502 KB)
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Biol.Unit 1 (131 KB)
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Biol.Unit 2 (131 KB)
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Biol.Unit 3 (129 KB)
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