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2WZS
Asym. Unit
Info
Asym.Unit (996 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (138 KB)
Biol.Unit 3 (137 KB)
Biol.Unit 4 (139 KB)
Biol.Unit 5 (135 KB)
Biol.Unit 6 (134 KB)
Biol.Unit 7 (131 KB)
Biol.Unit 8 (132 KB)
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(1)
Title
:
STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT3990 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 IN COMPLEX WITH MANNOIMIDAZOLE
Authors
:
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
Date
:
02 Dec 09 (Deposition) - 29 Dec 09 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
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)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Glycoside Hydrolase Family 92, Alpha-1, 2 Linkage, Bt3990, Hydrolase
(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
[
close entry info
]
Hetero Components
(3, 35)
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)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
3a: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLa)
3b: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLb)
3c: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLc)
3d: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLd)
3e: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLe)
3f: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLf)
3g: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLg)
3h: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
GOL
19
Ligand/Ion
GLYCEROL
3
MVL
8
Ligand/Ion
(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM
[
close Hetero Component info
]
Sites
(35, 35)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:601 , GLN A:602 , ASP A:644 , MVL A:801 , HOH A:2271 , HOH A:2283 , HOH A:2306
BINDING SITE FOR RESIDUE CA A 800
02
AC2
SOFTWARE
SER A:86 , TRP A:88 , 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:2267 , HOH A:2271 , HOH A:2306 , HOH A:2349
BINDING SITE FOR RESIDUE MVL A 801
03
AC3
SOFTWARE
LYS A:288 , TYR A:361 , VAL A:364 , GLU A:684
BINDING SITE FOR RESIDUE GOL A 802
04
AC4
SOFTWARE
LYS A:619
BINDING SITE FOR RESIDUE GOL A 803
05
AC5
SOFTWARE
GLU A:272 , HOH A:2147
BINDING SITE FOR RESIDUE GOL A 804
06
AC6
SOFTWARE
ASN B:601 , GLN B:602 , ASP B:644 , MVL B:801 , HOH B:2233 , HOH B:2241 , HOH B:2265
BINDING SITE FOR RESIDUE CA B 800
07
AC7
SOFTWARE
SER B:86 , TRP B:88 , ILE B:89 , TRP B:347 , ASP B:348 , TRP B:385 , CYS B:393 , MET B:394 , GLU B:533 , GLU B:585 , ASN B:601 , GLN B:602 , ASP B:644 , CA B:800 , HOH B:2265 , HOH B:2318
BINDING SITE FOR RESIDUE MVL B 801
08
AC8
SOFTWARE
LYS B:288 , GLU B:684
BINDING SITE FOR RESIDUE GOL B 802
09
AC9
SOFTWARE
TYR B:126 , GLU B:272 , HOH B:2319
BINDING SITE FOR RESIDUE GOL B 803
10
BC1
SOFTWARE
LYS B:315 , TYR B:317 , GLU B:367 , HOH B:2059
BINDING SITE FOR RESIDUE GOL B 804
11
BC2
SOFTWARE
ASN B:42 , THR B:43 , TYR B:44 , GLY B:66 , GLN B:84 , PRO B:85 , SER B:86 , PRO B:87 , HOH B:2320
BINDING SITE FOR RESIDUE GOL B 805
12
BC3
SOFTWARE
ASN C:601 , GLN C:602 , ASP C:644 , MVL C:801 , HOH C:2210 , HOH C:2278 , HOH C:2279
BINDING SITE FOR RESIDUE CA C 800
13
BC4
SOFTWARE
SER C:86 , TRP C:88 , TRP C:347 , ASP C:348 , TRP C:385 , GLU C:533 , GLU C:585 , ASN C:601 , GLN C:602 , ASP C:644 , CA C:800 , HOH C:2232 , HOH C:2278 , HOH C:2279
BINDING SITE FOR RESIDUE MVL C 801
14
BC5
SOFTWARE
GLN C:284 , LYS C:288 , VAL C:364 , GLU C:684
BINDING SITE FOR RESIDUE GOL C 802
15
BC6
SOFTWARE
LYS C:619 , TYR C:622 , TYR C:702
BINDING SITE FOR RESIDUE GOL C 803
16
BC7
SOFTWARE
TRP C:88 , CYS C:393
BINDING SITE FOR RESIDUE GOL C 804
17
BC8
SOFTWARE
GLU C:272
BINDING SITE FOR RESIDUE GOL C 805
18
BC9
SOFTWARE
ASN D:601 , GLN D:602 , ASP D:644 , MVL D:801 , HOH D:2236 , HOH D:2259 , HOH D:2261
BINDING SITE FOR RESIDUE CA D 800
19
CC1
SOFTWARE
SER D:86 , TRP D:88 , TRP D:347 , ASP D:348 , TRP D:385 , CYS D:393 , MET D:394 , GLU D:533 , GLU D:585 , ASN D:601 , GLN D:602 , ASP D:644 , CA D:800 , HOH D:2233 , HOH D:2258 , HOH D:2261
BINDING SITE FOR RESIDUE MVL D 801
20
CC2
SOFTWARE
ASN D:195 , LYS D:197 , TYR D:199 , ILE D:254 , VAL D:335 , HOH D:2101
BINDING SITE FOR RESIDUE GOL D 802
21
CC3
SOFTWARE
TYR D:622 , TYR D:702
BINDING SITE FOR RESIDUE GOL D 803
22
CC4
SOFTWARE
GLU D:272 , ALA D:275
BINDING SITE FOR RESIDUE GOL D 804
23
CC5
SOFTWARE
GLN D:284 , LYS D:288 , VAL D:364 , GLU D:684
BINDING SITE FOR RESIDUE GOL D 805
24
CC6
SOFTWARE
ASN E:601 , GLN E:602 , ASP E:644 , MVL E:801 , HOH E:2215 , HOH E:2238 , HOH E:2239
BINDING SITE FOR RESIDUE CA E 800
25
CC7
SOFTWARE
SER E:86 , TRP E:88 , TRP E:347 , ASP E:348 , TRP E:385 , CYS E:393 , MET E:394 , GLU E:533 , GLU E:585 , ASN E:601 , GLN E:602 , ASP E:644 , CA E:800 , HOH E:2215 , HOH E:2238 , HOH E:2260
BINDING SITE FOR RESIDUE MVL E 801
26
CC8
SOFTWARE
GLN E:284 , LYS E:288 , VAL E:364 , GLU E:684
BINDING SITE FOR RESIDUE GOL E 802
27
CC9
SOFTWARE
TYR E:702
BINDING SITE FOR RESIDUE GOL E 803
28
DC1
SOFTWARE
ASN E:358 , PRO E:362 , LYS E:409 , HIS E:720 , PHE E:724 , HOH E:2261
BINDING SITE FOR RESIDUE GOL E 804
29
DC2
SOFTWARE
ASN F:601 , GLN F:602 , ASP F:644 , MVL F:801 , HOH F:2172 , HOH F:2173
BINDING SITE FOR RESIDUE CA F 800
30
DC3
SOFTWARE
SER F:86 , TRP F:88 , ASP F:348 , TRP F:385 , CYS F:393 , GLU F:533 , GLU F:585 , ASN F:601 , GLN F:602 , ASP F:644 , CA F:800 , HOH F:2151 , HOH F:2172 , HOH F:2179
BINDING SITE FOR RESIDUE MVL F 801
31
DC4
SOFTWARE
GLU F:272 , ALA F:275
BINDING SITE FOR RESIDUE GOL F 802
32
DC5
SOFTWARE
ASN G:601 , GLN G:602 , ASP G:644 , MVL G:801 , HOH G:2072 , HOH G:2074
BINDING SITE FOR RESIDUE CA G 800
33
DC6
SOFTWARE
SER G:86 , TRP G:88 , TRP G:347 , ASP G:348 , TRP G:385 , CYS G:393 , MET G:394 , GLU G:533 , GLU G:585 , ASN G:601 , GLN G:602 , ASP G:644 , CA G:800 , HOH G:2072 , HOH G:2087
BINDING SITE FOR RESIDUE MVL G 801
34
DC7
SOFTWARE
ASN H:601 , GLN H:602 , ASP H:644 , MVL H:801 , HOH H:2057 , HOH H:2070
BINDING SITE FOR RESIDUE CA H 800
35
DC8
SOFTWARE
SER H:86 , TRP H:88 , TRP H:347 , ASP H:348 , TRP H:385 , GLU H:533 , GLU H:585 , ASN H:601 , GLN H:602 , ASP H:644 , CA H:800 , HOH H:2070
BINDING SITE FOR RESIDUE MVL H 801
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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
[
close SCOP info
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CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_2wzsA02 (A:289-312,A:607-631,A:632-748)
1b: CATH_2wzsB02 (B:289-312,B:607-631,B:632-748)
1c: CATH_2wzsC02 (C:289-312,C:607-631,C:632-748)
1d: CATH_2wzsD02 (D:289-312,D:607-631,D:632-748)
1e: CATH_2wzsE02 (E:289-312,E:607-631,E:632-748)
1f: CATH_2wzsF02 (F:289-312,F:607-631,F:632-748)
1g: CATH_2wzsG02 (G:289-312,G:607-631,G:632-748)
1h: CATH_2wzsH02 (H:289-312,H:607-631,H:632-748)
2a: CATH_2wzsA03 (A:344-438)
2b: CATH_2wzsB03 (B:344-438)
2c: CATH_2wzsC03 (C:344-438)
2d: CATH_2wzsD03 (D:344-438)
2e: CATH_2wzsE03 (E:344-438)
2f: CATH_2wzsF03 (F:344-438)
2g: CATH_2wzsG03 (G:344-438)
2h: CATH_2wzsH03 (H:344-438)
3a: CATH_2wzsA01 (A:20-53,A:54-288,A:313-343)
3b: CATH_2wzsB01 (B:20-53,B:54-288,B:313-343)
3c: CATH_2wzsC01 (C:20-53,C:54-288,C:313-343)
3d: CATH_2wzsD01 (D:20-53,D:54-288,D:313-343)
3e: CATH_2wzsE01 (E:20-53,E:54-288,E:313-343)
3f: CATH_2wzsF01 (F:20-53,F:54-288,F:313-343)
3g: CATH_2wzsG01 (G:20-53,G:54-288,G:313-343)
3h: CATH_2wzsH01 (H:20-53,H:54-288,H: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
2wzsA02
A:289-312,A:607-631,A:632-748
1b
2wzsB02
B:289-312,B:607-631,B:632-748
1c
2wzsC02
C:289-312,C:607-631,C:632-748
1d
2wzsD02
D:289-312,D:607-631,D:632-748
1e
2wzsE02
E:289-312,E:607-631,E:632-748
1f
2wzsF02
F:289-312,F:607-631,F:632-748
1g
2wzsG02
G:289-312,G:607-631,G:632-748
1h
2wzsH02
H:289-312,H:607-631,H: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
2wzsA03
A:344-438
2b
2wzsB03
B:344-438
2c
2wzsC03
C:344-438
2d
2wzsD03
D:344-438
2e
2wzsE03
E:344-438
2f
2wzsF03
F:344-438
2g
2wzsG03
G:344-438
2h
2wzsH03
H: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
2wzsA01
A:20-53,A:54-288,A:313-343
3b
2wzsB01
B:20-53,B:54-288,B:313-343
3c
2wzsC01
C:20-53,C:54-288,C:313-343
3d
2wzsD01
D:20-53,D:54-288,D:313-343
3e
2wzsE01
E:20-53,E:54-288,E:313-343
3f
2wzsF01
F:20-53,F:54-288,F:313-343
3g
2wzsG01
G:20-53,G:54-288,G:313-343
3h
2wzsH01
H:20-53,H:54-288,H:313-343
[
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]
Pfam Domains
(0, 0)
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