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2BFG
Asym. Unit
Info
Asym.Unit (693 KB)
Biol.Unit 1 (346 KB)
Biol.Unit 2 (348 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETA-XYLOSIDASE (FAM GH39) IN COMPLEX WITH DINITROPHENYL-BETA-XYLOSIDE AND COVALENTLY BOUND XYLOSIDE
Authors
:
M. Czjzek, T. Bravman, B. Henrissat, Y. Shoham
Date
:
07 Dec 04 (Deposition) - 12 Oct 05 (Release) - 14 Nov 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Hydrolase, Family Gh39, Thermophilic Enzyme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Czjzek, A. B. David, T. Bravman, G. Shoham, B. Henrissat, Y. Shoham
Enzyme-Substrate Complex Structures Of A Gh39 Beta- Xylosidase From Geobacillus Stearothermophilus.
J. Mol. Biol. V. 353 838 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 28)
Info
All Hetero Components
1a: 2,5-DINITROPHENOL (ANXa)
1b: 2,5-DINITROPHENOL (ANXb)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
4a: BETA-D-XYLOPYRANOSE (XYPa)
4b: BETA-D-XYLOPYRANOSE (XYPb)
5a: XYLOPYRANOSE (XYSa)
5b: XYLOPYRANOSE (XYSb)
5c: XYLOPYRANOSE (XYSc)
5d: XYLOPYRANOSE (XYSd)
5e: XYLOPYRANOSE (XYSe)
5f: XYLOPYRANOSE (XYSf)
5g: XYLOPYRANOSE (XYSg)
5h: XYLOPYRANOSE (XYSh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANX
2
Ligand/Ion
2,5-DINITROPHENOL
2
NA
8
Ligand/Ion
SODIUM ION
3
SO4
8
Ligand/Ion
SULFATE ION
4
XYP
2
Ligand/Ion
BETA-D-XYLOPYRANOSE
5
XYS
8
Ligand/Ion
XYLOPYRANOSE
[
close Hetero Component info
]
Sites
(26, 26)
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 (not defined)
24: CC6 (not defined)
25: CC7 (not defined)
26: CC8 (not defined)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:54 , PHE A:115 , ASN A:159 , TYR A:230 , GLU A:278 , TYR A:283 , TRP A:316 , GLU A:324 , PHE A:336 , ANX A:1504 , XYP A:1505
BINDING SITE FOR RESIDUE XYS B1504
02
AC2
SOFTWARE
HIS B:54 , PHE B:115 , ASN B:159 , HIS B:228 , TYR B:230 , GLU B:278 , TYR B:283 , TRP B:316 , GLU B:324 , PHE B:336
BINDING SITE FOR RESIDUE XYS C1504
03
AC3
SOFTWARE
HIS C:54 , PHE C:115 , ASN C:159 , PHE C:166 , HIS C:228 , TYR C:230 , GLU C:278 , TYR C:283 , TRP C:316 , PHE C:322 , GLU C:324 , PHE C:336
BINDING SITE FOR RESIDUE XYS E1504
04
AC4
SOFTWARE
HIS D:54 , PHE D:115 , ASN D:159 , PHE D:166 , HIS D:228 , TYR D:230 , GLU D:278 , TYR D:283 , TRP D:316 , GLU D:324 , PHE D:336 , ANX D:1504 , XYP D:1505
BINDING SITE FOR RESIDUE XYS F1504
05
AC5
SOFTWARE
HIS E:54 , PHE E:115 , ASN E:159 , PHE E:166 , HIS E:228 , TYR E:230 , GLU E:278 , TYR E:283 , TRP E:316 , GLU E:324 , PHE E:336
BINDING SITE FOR RESIDUE XYS G1504
06
AC6
SOFTWARE
HIS F:54 , PHE F:115 , ASN F:159 , PHE F:166 , TYR F:230 , GLU F:278 , TYR F:283 , TRP F:316 , GLU F:324 , PHE F:336
BINDING SITE FOR RESIDUE XYS H1504
07
AC7
SOFTWARE
HIS G:54 , PHE G:115 , ASN G:159 , HIS G:228 , TYR G:230 , GLU G:278 , TYR G:283 , TRP G:316 , GLU G:324 , PHE G:336
BINDING SITE FOR RESIDUE NA A1503
08
AC8
SOFTWARE
HIS H:54 , PHE H:115 , ASN H:159 , PHE H:166 , TYR H:230 , GLU H:278 , TYR H:283 , TRP H:316 , GLU H:324 , PHE H:336 , HOH H:2193
BINDING SITE FOR RESIDUE NA B1503
09
AC9
SOFTWARE
ARG D:26 , TRP D:117 , GLU D:323 , GLU D:324
BINDING SITE FOR RESIDUE SO4 B1505
10
BC1
SOFTWARE
GLY A:359 , ASP A:360 , ARG A:374 , LYS A:375 , HOH A:2172
BINDING SITE FOR RESIDUE NA C1503
11
BC2
SOFTWARE
ARG E:26 , TRP E:117 , GLU E:323 , GLU E:324 , HOH E:2124
BINDING SITE FOR RESIDUE SO4 C1505
12
BC3
SOFTWARE
GLY B:359 , ASP B:360 , ARG B:374 , LYS B:375 , HOH B:2167
BINDING SITE FOR RESIDUE NA D1503
13
BC4
SOFTWARE
ARG G:26 , LEU G:29 , TRP G:117 , GLU G:323 , GLU G:324
BINDING SITE FOR RESIDUE NA E1503
14
BC5
SOFTWARE
GLY C:359 , ASP C:360 , ARG C:374 , LYS C:375
BINDING SITE FOR RESIDUE SO4 E1505
15
BC6
SOFTWARE
ARG C:26 , TRP C:117 , GLU C:323 , GLU C:324
BINDING SITE FOR RESIDUE NA F1503
16
BC7
SOFTWARE
GLY D:359 , ASP D:360 , ARG D:374 , LYS D:375 , HOH D:2160
BINDING SITE FOR RESIDUE SO4 F1505
17
BC8
SOFTWARE
ARG B:26 , TRP B:117 , GLU B:323 , GLU B:324 , HOH B:2104
BINDING SITE FOR RESIDUE NA G1503
18
BC9
SOFTWARE
GLY E:359 , ASP E:360 , ARG E:373 , ARG E:374 , LYS E:375
BINDING SITE FOR RESIDUE SO4 G1505
19
CC1
SOFTWARE
ARG H:26 , TRP H:117 , GLU H:323 , HOH H:2122
BINDING SITE FOR RESIDUE NA H1503
20
CC2
SOFTWARE
GLY F:359 , ASP F:360 , ARG F:374 , LYS F:375
BINDING SITE FOR RESIDUE SO4 H1505
21
CC3
SOFTWARE
ARG A:26 , TRP A:117 , GLU A:323 , GLU A:324
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1504 TO 1507
22
CC4
SOFTWARE
GLY G:359 , ASP G:360 , ARG G:374 , LYS G:375 , HOH G:2178
BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 1504 TO 1507
23
CC5
not defined
ARG F:26 , TRP F:117 , GLU F:323
24
CC6
not defined
GLY H:359 , ASP H:360 , ARG H:374 , LYS H:375
25
CC7
not defined
HIS A:54 , PHE A:115 , ASN A:159 , LEU A:163 , PHE A:166 , CYS A:201 , HIS A:228 , TYR A:230 , GLU A:278 , TYR A:283 , TRP A:316 , GLU A:324 , PHE A:336 , XYS A:1507 , HOH A:2169 , HOH A:2170
26
CC8
not defined
HIS D:54 , PHE D:115 , ASN D:159 , LEU D:163 , PHE D:166 , CYS D:201 , HIS D:228 , TYR D:230 , GLU D:278 , TYR D:283 , TRP D:316 , GLU D:324 , PHE D:336 , XYS D:1507
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F39 (A:153-162,B:153-162,C:153-162,D:15...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F39
PS01027
Glycosyl hydrolases family 39 active site.
XYNB_GEOSE
153-162
8
A:153-162
B:153-162
C:153-162
D:153-162
E:153-162
F:153-162
G:153-162
H:153-162
[
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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, 16)
Info
All SCOP Domains
1a: SCOP_d2bfga1 (A:4-13,A:361-502)
1b: SCOP_d2bfgb1 (B:2-13,B:361-502)
1c: SCOP_d2bfgc1 (C:2-13,C:361-502)
1d: SCOP_d2bfgd1 (D:2-13,D:361-502)
1e: SCOP_d2bfge1 (E:2-13,E:361-502)
1f: SCOP_d2bfgf1 (F:2-13,F:361-502)
1g: SCOP_d2bfgg1 (G:2-13,G:361-502)
1h: SCOP_d2bfgh1 (H:2-13,H:361-502)
2a: SCOP_d2bfga2 (A:14-360)
2b: SCOP_d2bfgb2 (B:14-360)
2c: SCOP_d2bfgc2 (C:14-360)
2d: SCOP_d2bfgd2 (D:14-360)
2e: SCOP_d2bfge2 (E:14-360)
2f: SCOP_d2bfgf2 (F:14-360)
2g: SCOP_d2bfgg2 (G:14-360)
2h: SCOP_d2bfgh2 (H:14-360)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Glycosyl hydrolase domain
(397)
Superfamily
:
Glycosyl hydrolase domain
(397)
Family
:
Composite domain of glycosyl hydrolase families 5, 30, 39 and 51
(30)
Protein domain
:
Beta-D-xylosidase
(5)
Bacillus stearothermophilus [TaxId: 1422]
(3)
1a
d2bfga1
A:4-13,A:361-502
1b
d2bfgb1
B:2-13,B:361-502
1c
d2bfgc1
C:2-13,C:361-502
1d
d2bfgd1
D:2-13,D:361-502
1e
d2bfge1
E:2-13,E:361-502
1f
d2bfgf1
F:2-13,F:361-502
1g
d2bfgg1
G:2-13,G:361-502
1h
d2bfgh1
H:2-13,H:361-502
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
Beta-D-xylosidase, catalytic domain
(5)
Bacillus stearothermophilus [TaxId: 1422]
(3)
2a
d2bfga2
A:14-360
2b
d2bfgb2
B:14-360
2c
d2bfgc2
C:14-360
2d
d2bfgd2
D:14-360
2e
d2bfge2
E:14-360
2f
d2bfgf2
F:14-360
2g
d2bfgg2
G:14-360
2h
d2bfgh2
H:14-360
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_2bfgA02 (A:15-359)
1b: CATH_2bfgC02 (C:15-359)
1c: CATH_2bfgD02 (D:15-359)
1d: CATH_2bfgE02 (E:15-359)
1e: CATH_2bfgF02 (F:15-359)
1f: CATH_2bfgG02 (G:15-359)
1g: CATH_2bfgH02 (H:15-359)
1h: CATH_2bfgB02 (B:15-359)
2a: CATH_2bfgA01 (A:2-14,A:360-482)
2b: CATH_2bfgC01 (C:2-14,C:360-482)
2c: CATH_2bfgD01 (D:2-14,D:360-482)
2d: CATH_2bfgE01 (E:2-14,E:360-482)
2e: CATH_2bfgF01 (F:2-14,F:360-482)
2f: CATH_2bfgG01 (G:2-14,G:360-482)
2g: CATH_2bfgH01 (H:2-14,H:360-482)
2h: CATH_2bfgB01 (B:2-14,B:360-482)
View:
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(
)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Bacillus stearothermophilus. Organism_taxid: 1422. Strain: t-6.
(2)
1a
2bfgA02
A:15-359
1b
2bfgC02
C:15-359
1c
2bfgD02
D:15-359
1d
2bfgE02
E:15-359
1e
2bfgF02
F:15-359
1f
2bfgG02
G:15-359
1g
2bfgH02
H:15-359
1h
2bfgB02
B:15-359
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Glycosyl hydrolase domain; family 39
(5)
Bacillus stearothermophilus. Organism_taxid: 1422. Strain: t-6.
(2)
2a
2bfgA01
A:2-14,A:360-482
2b
2bfgC01
C:2-14,C:360-482
2c
2bfgD01
D:2-14,D:360-482
2d
2bfgE01
E:2-14,E:360-482
2e
2bfgF01
F:2-14,F:360-482
2f
2bfgG01
G:2-14,G:360-482
2g
2bfgH01
H:2-14,H:360-482
2h
2bfgB01
B:2-14,B:360-482
[
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]
Pfam Domains
(0, 0)
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