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.
2D1Z
Asym. Unit
Info
Asym.Unit (156 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (79 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF CATALYTIC-SITE MUTANT XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86
Authors
:
R. Suzuki, A. Kuno, Z. Fujimoto, S. Ito, S. I. Kawahara, S. Kaneko, T. Has K. Taira
Date
:
02 Sep 05 (Deposition) - 10 Oct 06 (Release) - 15 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tim-Barrel, Retaining Enzyme, Catalytic-Site Mutant, Chemical Rescue, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Suzuki, Z. Fujimoto, S. Ito, S. Kawahara, S. Kaneko, K. Taira, T. Hasegawa, A. Kuno
Crystallographic Snapshots Of An Entire Reaction Cycle For Retaining Xylanase From Streptomyces Olivaceoviridis E-86
J. Biochem. V. 146 61 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
2a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
11
Ligand/Ion
GLYCEROL
2
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER B:631 , ARG B:639 , ASP B:640 , HOH B:2005 , HOH B:2094 , HOH B:2299
BINDING SITE FOR RESIDUE SO4 A 1441
02
AC2
SOFTWARE
SER A:131 , ASP A:132 , ARG A:139 , ASP A:140
BINDING SITE FOR RESIDUE GOL A 1442
03
AC3
SOFTWARE
TYR A:172 , ASN A:173 , HIS A:207 , ASN A:209 , ARG A:275 , HOH A:1571 , HOH A:1820 , HOH A:1847
BINDING SITE FOR RESIDUE GOL A 1443
04
AC4
SOFTWARE
GLU A:357 , ARG A:359 , TRP A:383 , GLY A:384 , HOH A:1528 , HOH A:1676 , HOH A:1709 , ALA B:855 , GLU B:857 , GLY B:884 , LYS B:889
BINDING SITE FOR RESIDUE GOL A 1444
05
AC5
SOFTWARE
ASP A:408 , ALA A:409 , GLY A:411 , GLY A:412 , GLN A:421 , TYR A:423 , ASN A:430
BINDING SITE FOR RESIDUE GOL A 1445
06
AC6
SOFTWARE
ASP A:325 , VAL A:326 , PRO A:327 , ASN A:328 , GLN A:338 , TYR A:340 , HIS A:343 , ASN A:347 , HOH A:1660 , HOH A:1870
BINDING SITE FOR RESIDUE GOL A 1446
07
AC7
SOFTWARE
SER B:597 , ARG B:645 , HOH B:1986 , HOH B:2206 , HOH B:2233
BINDING SITE FOR RESIDUE GOL B 1941
08
AC8
SOFTWARE
LYS B:548 , TRP B:585 , GLN B:588 , HIS B:628 , HOH B:2109 , HOH B:2391 , HOH B:2394
BINDING SITE FOR RESIDUE GOL B 1942
09
AC9
SOFTWARE
LYS B:524 , THR B:771 , ASP B:772 , SER B:773 , HOH B:1978 , HOH B:2097 , HOH B:2189
BINDING SITE FOR RESIDUE GOL B 1943
10
BC1
SOFTWARE
TYR B:672 , ASN B:673 , HIS B:707 , ASN B:709 , ARG B:775 , HOH B:2109 , HOH B:2261 , HOH B:2418
BINDING SITE FOR RESIDUE GOL B 1944
11
BC2
SOFTWARE
ASP B:825 , ASN B:828 , TYR B:840 , HIS B:843 , ASN B:847 , HOH B:2369
BINDING SITE FOR RESIDUE GOL B 1945
12
BC3
SOFTWARE
ASP B:908 , ALA B:909 , VAL B:910 , GLY B:911 , GLY B:912 , GLN B:921 , TYR B:923 , ASN B:930
BINDING SITE FOR RESIDUE GOL B 1946
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d2d1za2 (A:322-436)
1b: SCOP_d2d1zb2 (B:822-936)
2a: SCOP_d2d1za1 (A:1-301)
2b: SCOP_d2d1zb1 (B:501-801)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
automated matches
(21)
Protein domain
:
automated matches
(21)
Streptomyces olivaceoviridis [TaxId: 1921]
(5)
1a
d2d1za2
A:322-436
1b
d2d1zb2
B:822-936
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
automated matches
(49)
Streptomyces olivaceoviridis [TaxId: 1921]
(8)
2a
d2d1za1
A:1-301
2b
d2d1zb1
B:501-801
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2d1zA01 (A:1-300)
1b: CATH_2d1zB01 (B:501-800)
2a: CATH_2d1zA02 (A:313-434)
2b: CATH_2d1zB02 (B:813-934)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Streptomyces olivaceoviridis. Organism_taxid: 1921. Strain: e-86.
(13)
1a
2d1zA01
A:1-300
1b
2d1zB01
B:501-800
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Streptomyces olivaceoviridis. Organism_taxid: 1921. Strain: e-86.
(11)
2a
2d1zA02
A:313-434
2b
2d1zB02
B:813-934
[
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
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 (156 KB)
Header - Asym.Unit
Biol.Unit 1 (77 KB)
Header - Biol.Unit 1
Biol.Unit 2 (79 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
2D1Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help