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Biol. Unit 4
Info
Asym.Unit (534 KB)
Biol.Unit 1 (137 KB)
Biol.Unit 2 (137 KB)
Biol.Unit 3 (138 KB)
Biol.Unit 4 (137 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) - 03 Nov 09 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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
:
Glycoside Hydrolase Family 92, Gh92, Hydrolase, Bt3990
(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
(2, 31)
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)
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)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3ao: SELENOMETHIONINE (MSEao)
3ap: SELENOMETHIONINE (MSEap)
3aq: SELENOMETHIONINE (MSEaq)
3ar: SELENOMETHIONINE (MSEar)
3as: SELENOMETHIONINE (MSEas)
3at: SELENOMETHIONINE (MSEat)
3au: SELENOMETHIONINE (MSEau)
3av: SELENOMETHIONINE (MSEav)
3aw: SELENOMETHIONINE (MSEaw)
3ax: SELENOMETHIONINE (MSEax)
3ay: SELENOMETHIONINE (MSEay)
3az: SELENOMETHIONINE (MSEaz)
3b: SELENOMETHIONINE (MSEb)
3ba: SELENOMETHIONINE (MSEba)
3bb: SELENOMETHIONINE (MSEbb)
3bc: SELENOMETHIONINE (MSEbc)
3bd: SELENOMETHIONINE (MSEbd)
3be: SELENOMETHIONINE (MSEbe)
3bf: SELENOMETHIONINE (MSEbf)
3bg: SELENOMETHIONINE (MSEbg)
3bh: SELENOMETHIONINE (MSEbh)
3bi: SELENOMETHIONINE (MSEbi)
3bj: SELENOMETHIONINE (MSEbj)
3bk: SELENOMETHIONINE (MSEbk)
3bl: SELENOMETHIONINE (MSEbl)
3bm: SELENOMETHIONINE (MSEbm)
3bn: SELENOMETHIONINE (MSEbn)
3bo: SELENOMETHIONINE (MSEbo)
3bp: SELENOMETHIONINE (MSEbp)
3bq: SELENOMETHIONINE (MSEbq)
3br: SELENOMETHIONINE (MSEbr)
3bs: SELENOMETHIONINE (MSEbs)
3bt: SELENOMETHIONINE (MSEbt)
3bu: SELENOMETHIONINE (MSEbu)
3bv: SELENOMETHIONINE (MSEbv)
3bw: SELENOMETHIONINE (MSEbw)
3bx: SELENOMETHIONINE (MSEbx)
3by: SELENOMETHIONINE (MSEby)
3bz: SELENOMETHIONINE (MSEbz)
3c: SELENOMETHIONINE (MSEc)
3ca: SELENOMETHIONINE (MSEca)
3cb: SELENOMETHIONINE (MSEcb)
3cc: SELENOMETHIONINE (MSEcc)
3cd: SELENOMETHIONINE (MSEcd)
3ce: SELENOMETHIONINE (MSEce)
3cf: SELENOMETHIONINE (MSEcf)
3cg: SELENOMETHIONINE (MSEcg)
3ch: SELENOMETHIONINE (MSEch)
3ci: SELENOMETHIONINE (MSEci)
3cj: SELENOMETHIONINE (MSEcj)
3ck: SELENOMETHIONINE (MSEck)
3cl: SELENOMETHIONINE (MSEcl)
3cm: SELENOMETHIONINE (MSEcm)
3cn: SELENOMETHIONINE (MSEcn)
3co: SELENOMETHIONINE (MSEco)
3cp: SELENOMETHIONINE (MSEcp)
3cq: SELENOMETHIONINE (MSEcq)
3cr: SELENOMETHIONINE (MSEcr)
3cs: SELENOMETHIONINE (MSEcs)
3ct: SELENOMETHIONINE (MSEct)
3cu: SELENOMETHIONINE (MSEcu)
3cv: SELENOMETHIONINE (MSEcv)
3cw: SELENOMETHIONINE (MSEcw)
3cx: SELENOMETHIONINE (MSEcx)
3cy: SELENOMETHIONINE (MSEcy)
3cz: SELENOMETHIONINE (MSEcz)
3d: SELENOMETHIONINE (MSEd)
3da: SELENOMETHIONINE (MSEda)
3db: SELENOMETHIONINE (MSEdb)
3dc: SELENOMETHIONINE (MSEdc)
3dd: SELENOMETHIONINE (MSEdd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
MSE
27
Mod. Amino Acid
SELENOMETHIONINE
[
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]
Sites
(5, 5)
Info
All Sites
1: BC7 (SOFTWARE)
2: BC8 (SOFTWARE)
3: BC9 (SOFTWARE)
4: CC1 (SOFTWARE)
5: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC7
SOFTWARE
GLU D:533 , GLY D:600 , GLN D:602 , ASP D:644 , HOH D:2401
BINDING SITE FOR RESIDUE CA D 801
2
BC8
SOFTWARE
SER D:86 , ASP D:348 , TRP D:385 , MSE D:394 , ASP D:644 , HOH D:2430 , HOH D:2497
BINDING SITE FOR RESIDUE GOL D 803
3
BC9
SOFTWARE
LYS D:288 , VAL D:364 , GLU D:684 , HOH D:2265 , HOH D:2498
BINDING SITE FOR RESIDUE GOL D 804
4
CC1
SOFTWARE
GLY D:293 , GLN D:298 , LEU D:675 , ASN D:696 , SER D:697 , HOH D:2499
BINDING SITE FOR RESIDUE GOL D 805
5
CC2
SOFTWARE
TYR D:126 , GLU D:272 , ALA D:275
BINDING SITE FOR RESIDUE GOL D 806
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
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CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_2wvxA02 (A:289-312,A:608-630,A:632-747)
1b: CATH_2wvxB02 (B:289-312,B:608-630,B:632-747)
1c: CATH_2wvxC02 (C:289-312,C:608-630,C:632-747)
1d: CATH_2wvxD02 (D:289-312,D:608-630,D:632-747)
2a: CATH_2wvxA03 (A:344-438)
2b: CATH_2wvxB03 (B:344-438)
2c: CATH_2wvxC03 (C:344-438)
2d: CATH_2wvxD03 (D:344-438)
3a: CATH_2wvxA01 (A:20-52,A:54-288,A:313-343)
3b: CATH_2wvxB01 (B:20-52,B:54-288,B:313-343)
3c: CATH_2wvxC01 (C:20-52,C:54-288,C:313-343)
3d: CATH_2wvxD01 (D:20-52,D:54-288,D: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
2wvxA02
A:289-312,A:608-630,A:632-747
1b
2wvxB02
B:289-312,B:608-630,B:632-747
1c
2wvxC02
C:289-312,C:608-630,C:632-747
1d
2wvxD02
D:289-312,D:608-630,D:632-747
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
2wvxA03
A:344-438
2b
2wvxB03
B:344-438
2c
2wvxC03
C:344-438
2d
2wvxD03
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
2wvxA01
A:20-52,A:54-288,A:313-343
3b
2wvxB01
B:20-52,B:54-288,B:313-343
3c
2wvxC01
C:20-52,C:54-288,C:313-343
3d
2wvxD01
D:20-52,D:54-288,D:313-343
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_92_2wvxD01 (D:228-737)
1b: PFAM_Glyco_hydro_92_2wvxD02 (D:228-737)
1c: PFAM_Glyco_hydro_92_2wvxD03 (D:228-737)
1d: PFAM_Glyco_hydro_92_2wvxD04 (D:228-737)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_92
(7)
Bacteroides thetaiotaomicron
(7)
1a
Glyco_hydro_92-2wvxD01
D:228-737
1b
Glyco_hydro_92-2wvxD02
D:228-737
1c
Glyco_hydro_92-2wvxD03
D:228-737
1d
Glyco_hydro_92-2wvxD04
D:228-737
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Asym.Unit (534 KB)
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