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2WW3
Asym. Unit
Info
Asym.Unit (745 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (130 KB)
Biol.Unit 3 (134 KB)
Biol.Unit 4 (130 KB)
Biol.Unit 5 (132 KB)
Biol.Unit 6 (131 KB)
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(1)
Title
:
STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT3990 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 IN COMPLEX WITH THIOMANNOBIOSIDE
Authors
:
M. D. L. Suits, Y. Zhu, A. J. Thompson, H. J. Gilbert, G. J. Davies
Date
:
21 Oct 09 (Deposition) - 26 Jan 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Hydrolase, Glycoside Hydrolase Family 92, Gh92, Bt3990
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhu, M. D. L. Suits, A. J. 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 Ca(2+)-Dependent Family Of Alpha-Mannosidases In A Human Gut Symbiont.
Nat. Chem. Biol. V. 6 125 2010
[
close entry info
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDa)
3b: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDb)
3c: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDc)
3d: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDd)
3e: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDe)
3f: METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL... (SMDf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
GOL
3
Ligand/Ion
GLYCEROL
3
SMD
6
Ligand/Ion
METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D-MANNOPYRANOSIDE
[
close Hetero Component info
]
Sites
(15, 15)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:602 , ASP A:644 , SMD A:801 , HOH A:2161 , HOH A:2163
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 , MET A:394 , GLU A:533 , HIS A:584 , GLU A:585 , GLN A:602 , ASP A:642 , ASP A:644 , CA A:800
BINDING SITE FOR RESIDUE SMD A 801
03
AC3
SOFTWARE
GLU A:272 , ALA A:275
BINDING SITE FOR RESIDUE GOL A 802
04
AC4
SOFTWARE
GLN B:602 , ASP B:644 , SMD B:801 , HOH B:2123 , HOH B:2134
BINDING SITE FOR RESIDUE CA B 800
05
AC5
SOFTWARE
SER B:86 , TRP B:88 , ILE B:89 , TRP B:347 , ASP B:348 , TRP B:385 , MET B:394 , GLU B:533 , HIS B:584 , GLU B:585 , GLN B:602 , ASP B:642 , ASP B:644 , CA B:800
BINDING SITE FOR RESIDUE SMD B 801
06
AC6
SOFTWARE
GLN C:602 , ASP C:644 , SMD C:801 , HOH C:2257 , HOH C:2260
BINDING SITE FOR RESIDUE CA C 800
07
AC7
SOFTWARE
SER C:86 , TRP C:88 , TRP C:347 , ASP C:348 , TRP C:385 , CYS C:393 , MET C:394 , GLU C:533 , HIS C:584 , GLU C:585 , GLN C:602 , ASP C:642 , ASP C:644 , CA C:800 , HOH C:2322
BINDING SITE FOR RESIDUE SMD C 801
08
AC8
SOFTWARE
GLN C:284 , LYS C:288 , GLU C:684
BINDING SITE FOR RESIDUE GOL C 802
09
AC9
SOFTWARE
GLN D:602 , ASP D:644 , SMD D:801 , HOH D:2117
BINDING SITE FOR RESIDUE CA D 800
10
BC1
SOFTWARE
SER D:86 , TRP D:88 , TRP D:347 , ASP D:348 , TRP D:385 , MET D:394 , GLU D:533 , HIS D:584 , GLU D:585 , GLN D:602 , ASP D:642 , ASP D:644 , CA D:800
BINDING SITE FOR RESIDUE SMD D 801
11
BC2
SOFTWARE
ASP E:348 , GLN E:602 , ASP E:644 , SMD E:801 , HOH E:2148 , HOH E:2149
BINDING SITE FOR RESIDUE CA E 800
12
BC3
SOFTWARE
SER E:86 , TRP E:88 , ILE E:89 , TRP E:347 , ASP E:348 , TRP E:385 , MET E:394 , GLU E:533 , HIS E:584 , GLU E:585 , GLN E:602 , ASP E:642 , ASP E:644 , CA E:800
BINDING SITE FOR RESIDUE SMD E 801
13
BC4
SOFTWARE
GLN E:284 , LYS E:288 , TYR E:361 , VAL E:364 , GLU E:684 , HOH E:2217
BINDING SITE FOR RESIDUE GOL E 802
14
BC5
SOFTWARE
GLN F:602 , ASP F:644 , SMD F:801 , HOH F:2150
BINDING SITE FOR RESIDUE CA F 800
15
BC6
SOFTWARE
SER F:86 , TRP F:88 , ILE F:89 , TRP F:347 , ASP F:348 , TRP F:385 , CYS F:393 , MET F:394 , GLU F:533 , HIS F:584 , GLU F:585 , GLN F:602 , ASP F:642 , ASP F:644 , CA F:800 , HOH F:2195
BINDING SITE FOR RESIDUE SMD F 801
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_2ww3A02 (A:289-312,A:607-631,A:632-748)
1b: CATH_2ww3B02 (B:289-312,B:607-631,B:632-748)
1c: CATH_2ww3C02 (C:289-312,C:607-631,C:632-748)
1d: CATH_2ww3D02 (D:289-312,D:607-631,D:632-748)
1e: CATH_2ww3E02 (E:289-312,E:607-631,E:632-748)
1f: CATH_2ww3F02 (F:289-312,F:607-631,F:632-748)
2a: CATH_2ww3A03 (A:344-438)
2b: CATH_2ww3B03 (B:344-438)
2c: CATH_2ww3C03 (C:344-438)
2d: CATH_2ww3D03 (D:344-438)
2e: CATH_2ww3E03 (E:344-438)
2f: CATH_2ww3F03 (F:344-438)
3a: CATH_2ww3A01 (A:20-53,A:54-288,A:313-343)
3b: CATH_2ww3B01 (B:20-53,B:54-288,B:313-343)
3c: CATH_2ww3C01 (C:20-53,C:54-288,C:313-343)
3d: CATH_2ww3D01 (D:20-53,D:54-288,D:313-343)
3e: CATH_2ww3E01 (E:20-53,E:54-288,E:313-343)
3f: CATH_2ww3F01 (F:20-53,F:54-288,F:313-343)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
2ww3A02
A:289-312,A:607-631,A:632-748
1b
2ww3B02
B:289-312,B:607-631,B:632-748
1c
2ww3C02
C:289-312,C:607-631,C:632-748
1d
2ww3D02
D:289-312,D:607-631,D:632-748
1e
2ww3E02
E:289-312,E:607-631,E:632-748
1f
2ww3F02
F:289-312,F:607-631,F: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
2ww3A03
A:344-438
2b
2ww3B03
B:344-438
2c
2ww3C03
C:344-438
2d
2ww3D03
D:344-438
2e
2ww3E03
E:344-438
2f
2ww3F03
F: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
2ww3A01
A:20-53,A:54-288,A:313-343
3b
2ww3B01
B:20-53,B:54-288,B:313-343
3c
2ww3C01
C:20-53,C:54-288,C:313-343
3d
2ww3D01
D:20-53,D:54-288,D:313-343
3e
2ww3E01
E:20-53,E:54-288,E:313-343
3f
2ww3F01
F:20-53,F:54-288,F:313-343
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_92_2ww3F01 (F:228-737)
1b: PFAM_Glyco_hydro_92_2ww3F02 (F:228-737)
1c: PFAM_Glyco_hydro_92_2ww3F03 (F:228-737)
1d: PFAM_Glyco_hydro_92_2ww3F04 (F:228-737)
1e: PFAM_Glyco_hydro_92_2ww3F05 (F:228-737)
1f: PFAM_Glyco_hydro_92_2ww3F06 (F:228-737)
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Clans
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Organisms
(
)
(
)
Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_92
(7)
Bacteroides thetaiotaomicron
(7)
1a
Glyco_hydro_92-2ww3F01
F:228-737
1b
Glyco_hydro_92-2ww3F02
F:228-737
1c
Glyco_hydro_92-2ww3F03
F:228-737
1d
Glyco_hydro_92-2ww3F04
F:228-737
1e
Glyco_hydro_92-2ww3F05
F:228-737
1f
Glyco_hydro_92-2ww3F06
F:228-737
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Asym.Unit (745 KB)
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