PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2EXH
Asym. Unit
Info
Asym.Unit (395 KB)
Biol.Unit 1 (388 KB)
Biol.Unit 2 (388 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE FAMILY43 BETA-XYLOSIDASE FROM GEOBACILLUS STEAROTHERMOPHILUS
Authors
:
C. Brux, K. Niefind, D. Shallom-Shezifi, S. Yuval, D. Schomburg
Date
:
08 Nov 05 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.88
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (1x)
Keywords
:
Glykosidase, Hydrolsase, Xylosidase, Family43, 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
)
[
close entry info
]
Hetero Components
(3, 11)
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)
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
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:333 , GLY A:362 , ASP A:528 , HOH A:2125 , HOH A:2139
BINDING SITE FOR RESIDUE CA A 2001
02
AC2
SOFTWARE
ASP B:333 , GLY B:362 , ASP B:528 , HOH B:2113 , HOH B:2162 , HOH B:2308
BINDING SITE FOR RESIDUE CA B 2002
03
AC3
SOFTWARE
ASP C:333 , GLY C:362 , ASP C:528 , HOH C:2101 , HOH C:2113
BINDING SITE FOR RESIDUE CA C 2003
04
AC4
SOFTWARE
ASP D:333 , GLY D:362 , ASP D:528 , HOH D:2138
BINDING SITE FOR RESIDUE CA D 2004
05
AC5
SOFTWARE
VAL A:52 , ALA A:53 , ARG A:54 , HIS A:341 , HOH A:2316 , HIS B:389 , GLN B:468 , LEU B:535
BINDING SITE FOR RESIDUE MES A 2005
06
AC6
SOFTWARE
LEU B:51 , VAL B:52 , ARG B:54 , ASN B:57 , ASP B:113 , GLY B:114 , HIS B:341
BINDING SITE FOR RESIDUE MES B 2006
07
AC7
SOFTWARE
LEU D:51 , VAL D:52 , ALA D:53 , ARG D:54 , ASN D:57 , ASP D:113 , HIS D:341
BINDING SITE FOR RESIDUE MES D 2007
08
AC8
SOFTWARE
SER A:60 , GLN A:61 , ASN A:63 , ASP A:91 , TYR A:105 , PRO A:119 , HOH A:2134 , HOH A:2425
BINDING SITE FOR RESIDUE GOL A 2008
09
AC9
SOFTWARE
SER B:60 , GLN B:61 , LEU B:62 , ASN B:63 , ASP B:91 , TYR B:105 , PRO B:119 , HOH B:2124 , HOH B:2467
BINDING SITE FOR RESIDUE GOL B 2009
10
BC1
SOFTWARE
SER C:60 , LEU C:62 , ASN C:63 , ASP C:91 , TYR C:105 , PRO C:119 , HOH C:2307
BINDING SITE FOR RESIDUE GOL C 2010
11
BC2
SOFTWARE
SER D:60 , GLN D:61 , LEU D:62 , ASN D:63 , ASP D:91 , TYR D:105 , PRO D:119 , HOH D:2033
BINDING SITE FOR RESIDUE GOL D 2011
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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_d2exha2 (A:3-324)
1b: SCOP_d2exhb2 (B:3-324)
1c: SCOP_d2exhc2 (C:3-324)
1d: SCOP_d2exhd2 (D:3-324)
2a: SCOP_d2exha1 (A:325-535)
2b: SCOP_d2exhb1 (B:325-535)
2c: SCOP_d2exhc1 (C:325-535)
2d: SCOP_d2exhd1 (D:325-535)
View:
Select:
Label:
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
d2exha2
A:3-324
1b
d2exhb2
B:3-324
1c
d2exhc2
C:3-324
1d
d2exhd2
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
d2exha1
A:325-535
2b
d2exhb1
B:325-535
2c
d2exhc1
C:325-535
2d
d2exhd1
D:325-535
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2exhA01 (A:3-327)
1b: CATH_2exhB01 (B:3-327)
1c: CATH_2exhC01 (C:3-327)
1d: CATH_2exhD01 (D:3-327)
2a: CATH_2exhA02 (A:328-535)
2b: CATH_2exhB02 (B:328-535)
2c: CATH_2exhC02 (C:328-535)
2d: CATH_2exhD02 (D:328-535)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2exhA01
A:3-327
1b
2exhB01
B:3-327
1c
2exhC01
C:3-327
1d
2exhD01
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
2exhA02
A:328-535
2b
2exhB02
B:328-535
2c
2exhC02
C:328-535
2d
2exhD02
D:328-535
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (395 KB)
Header - Asym.Unit
Biol.Unit 1 (388 KB)
Header - Biol.Unit 1
Biol.Unit 2 (388 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2EXH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help