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2EXK
Asym. Unit
Info
Asym.Unit (381 KB)
Biol.Unit 1 (373 KB)
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(1)
Title
:
STRUCTURE OF THE FAMILY43 BETA-XYLOSIDASE E187G FROM GEOBACILLUS STEAROTHERMOPHILUS IN COMPLEX WITH XYLOBIOSE
Authors
:
C. Brux, K. Niefind, D. Shallom-Shezifi, Y. Shoham, D. Schomburg
Date
:
08 Nov 05 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Glykosidase, Hydrolsase, Xylosidase, Family43, Xylose, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Brux, A. Ben-David, D. Shallom-Shezifi, M. Leon, K. Niefind, G. Shoham, Y. Shoham, D. Schomburg
The Structure Of An Inverting Gh43 Beta-Xylosidase From Geobacillus Stearothermophilus With Its Substrate Reveals The Role Of The Three Catalytic Residues.
J. Mol. Biol. V. 359 97 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 19)
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)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
3c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
4a: XYLOPYRANOSE (XYSa)
4b: XYLOPYRANOSE (XYSb)
4c: XYLOPYRANOSE (XYSc)
4d: XYLOPYRANOSE (XYSd)
4e: XYLOPYRANOSE (XYSe)
4f: XYLOPYRANOSE (XYSf)
4g: XYLOPYRANOSE (XYSg)
4h: XYLOPYRANOSE (XYSh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
MES
3
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
XYS
8
Ligand/Ion
XYLOPYRANOSE
[
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]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:15 , PHE A:32 , TRP A:74 , ALA A:75 , PHE A:127 , ASP A:128 , ARG A:288 , PHE A:506 , XYS A:2006 , HOH A:2136
BINDING SITE FOR RESIDUE XYS A 2005
02
AC2
SOFTWARE
PHE A:127 , GLY A:206 , THR A:207 , XYS A:2005 , HOH A:2024 , HOH A:2096 , HOH A:2308
BINDING SITE FOR RESIDUE XYS A 2006
03
AC3
SOFTWARE
ASP B:15 , PHE B:32 , TRP B:74 , ALA B:75 , ASP B:128 , THR B:207 , HIS B:249 , ARG B:288 , PHE B:506 , XYS B:2008 , HOH B:2196
BINDING SITE FOR RESIDUE XYS B 2007
04
AC4
SOFTWARE
GLY B:206 , THR B:207 , PHE B:506 , XYS B:2007 , HOH B:2098 , HOH B:2183 , HOH B:2196
BINDING SITE FOR RESIDUE XYS B 2008
05
AC5
SOFTWARE
ASP C:15 , PHE C:32 , TRP C:74 , ALA C:75 , PHE C:127 , ASP C:128 , THR C:207 , ARG C:288 , PHE C:506 , XYS C:2010 , HOH C:2052 , HOH C:2088
BINDING SITE FOR RESIDUE XYS C 2009
06
AC6
SOFTWARE
TRP C:74 , GLY C:206 , THR C:207 , PHE C:506 , XYS C:2009 , HOH C:2052
BINDING SITE FOR RESIDUE XYS C 2010
07
AC7
SOFTWARE
ASP D:15 , PHE D:32 , TRP D:74 , ALA D:75 , PHE D:127 , ASP D:128 , ARG D:288 , PHE D:506 , XYS D:2012 , HOH D:2047
BINDING SITE FOR RESIDUE XYS D 2011
08
AC8
SOFTWARE
GLY D:206 , THR D:207 , XYS D:2011 , HOH D:2039 , HOH D:2047 , HOH D:2276
BINDING SITE FOR RESIDUE XYS D 2012
09
AC9
SOFTWARE
ASP A:333 , GLY A:362 , ASP A:528 , HOH A:2054 , HOH A:2062
BINDING SITE FOR RESIDUE CA A 2001
10
BC1
SOFTWARE
ASP B:333 , GLY B:362 , ASP B:528 , HOH B:2100 , HOH B:2255 , HOH B:2262
BINDING SITE FOR RESIDUE CA B 2002
11
BC2
SOFTWARE
ASP C:333 , GLY C:362 , ASP C:528 , HOH C:2080
BINDING SITE FOR RESIDUE CA C 2003
12
BC3
SOFTWARE
ASP D:333 , GLY D:362 , ASP D:528 , HOH D:2111
BINDING SITE FOR RESIDUE CA D 2004
13
BC4
SOFTWARE
VAL A:52 , ALA A:53 , ARG A:54 , HIS A:341 , HOH A:2044 , HOH A:2184 , HIS B:389 , GLN B:468 , LEU B:535
BINDING SITE FOR RESIDUE MES A 2013
14
BC5
SOFTWARE
LEU B:51 , VAL B:52 , ALA B:53 , ARG B:54 , ASN B:57 , GLY B:114 , HIS B:341
BINDING SITE FOR RESIDUE MES B 2014
15
BC6
SOFTWARE
LEU D:51 , VAL D:52 , ALA D:53 , ARG D:54 , ASN D:57 , ASP D:113 , GLY D:114 , HIS D:341 , HOH D:2230
BINDING SITE FOR RESIDUE MES D 2015
16
BC7
SOFTWARE
SER A:60 , GLN A:61 , LEU A:62 , ASN A:63 , ASP A:91 , TYR A:105 , PRO A:119 , HOH A:2282 , HOH A:2313
BINDING SITE FOR RESIDUE GOL A 2016
17
BC8
SOFTWARE
SER B:60 , GLN B:61 , LEU B:62 , ASN B:63 , ASP B:91 , TYR B:105 , PRO B:119 , HOH B:2378
BINDING SITE FOR RESIDUE GOL B 2017
18
BC9
SOFTWARE
SER C:60 , GLN C:61 , LEU C:62 , ASN C:63 , ASP C:91 , TYR C:105 , PRO C:119
BINDING SITE FOR RESIDUE GOL C 2018
19
CC1
SOFTWARE
SER D:60 , GLN D:61 , LEU D:62 , ASN D:63 , ASP D:91 , PRO D:119 , HOH D:2282
BINDING SITE FOR RESIDUE GOL D 2019
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2exka2 (A:3-324)
1b: SCOP_d2exkb2 (B:3-324)
1c: SCOP_d2exkc2 (C:3-324)
1d: SCOP_d2exkd2 (D:3-324)
2a: SCOP_d2exka1 (A:325-535)
2b: SCOP_d2exkb1 (B:325-535)
2c: SCOP_d2exkc1 (C:325-535)
2d: SCOP_d2exkd1 (D:325-535)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
5-bladed beta-propeller
(42)
Superfamily
:
Arabinanase/levansucrase/invertase
(37)
Family
:
alpha-L-arabinanase-like
(18)
Protein domain
:
Beta-D-xylosidase N-terminal domain
(8)
Geobacillus stearothermophilus [TaxId: 1422]
(4)
1a
d2exka2
A:3-324
1b
d2exkb2
B:3-324
1c
d2exkc2
C:3-324
1d
d2exkd2
D:3-324
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Beta-D-xylosidase C-terminal domain-like
(8)
Protein domain
:
Beta-D-xylosidase C-terminal domain
(8)
Geobacillus stearothermophilus [TaxId: 1422]
(4)
2a
d2exka1
A:325-535
2b
d2exkb1
B:325-535
2c
d2exkc1
C:325-535
2d
d2exkd1
D:325-535
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2exkA01 (A:3-327)
1b: CATH_2exkB01 (B:3-327)
1c: CATH_2exkC01 (C:3-327)
1d: CATH_2exkD01 (D:3-327)
2a: CATH_2exkA02 (A:328-535)
2b: CATH_2exkB02 (B:328-535)
2c: CATH_2exkC02 (C:328-535)
2d: CATH_2exkD02 (D:328-535)
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Topologies
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
5 Propellor
(21)
Topology
:
Tachylectin-2; Chain A
(21)
Homologous Superfamily
:
Glycosyl hydrolase domain; family 43
(20)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(4)
1a
2exkA01
A:3-327
1b
2exkB01
B:3-327
1c
2exkC01
C:3-327
1d
2exkD01
D:3-327
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(4)
2a
2exkA02
A:328-535
2b
2exkB02
B:328-535
2c
2exkC02
C:328-535
2d
2exkD02
D:328-535
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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