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.
5XIN
Asym. Unit
Info
Asym.Unit (271 KB)
Biol.Unit 1 (265 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES
Authors
:
J. Janin
Date
:
06 Apr 92 (Deposition) - 15 Jul 93 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Isomerase(Intramolecular Oxidoreductse)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Jenkins, J. Janin, F. Rey, M. Chiadmi, H. Van Tilbeurgh, I. Lasters, M. De Maeyer, D. Van Belle, S. J. Wodak, M. Lauwereys, P. Stanssens, G. Matthyssens, A. M. Lambeir
Protein Engineering Of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography And Site-Directed Mutagenesis Of Metal Binding Sites.
Biochemistry V. 31 5449 1992
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: D-XYLOSE (LINEAR FORM) (XLSa)
2b: D-XYLOSE (LINEAR FORM) (XLSb)
2c: D-XYLOSE (LINEAR FORM) (XLSc)
2d: D-XYLOSE (LINEAR FORM) (XLSd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
XLS
4
Ligand/Ion
D-XYLOSE (LINEAR FORM)
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:16 , HIS A:54 , TRP A:137 , GLU A:181 , LYS A:183 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:292 , MG A:395 , HOH A:454 , HOH A:455 , HOH A:539
BINDING SITE FOR RESIDUE XLS A 397
2
AC2
SOFTWARE
TRP B:16 , HIS B:54 , TRP B:137 , GLU B:181 , LYS B:183 , GLU B:217 , HIS B:220 , ASP B:245 , ASP B:292 , MG B:395 , HOH B:458 , HOH B:459
BINDING SITE FOR RESIDUE XLS B 397
3
AC3
SOFTWARE
TRP C:16 , HIS C:54 , PHE C:94 , TRP C:137 , GLU C:181 , GLU C:217 , HIS C:220 , ASP C:245 , ASP C:292 , MG C:395 , HOH C:467 , HOH C:468 , HOH C:622
BINDING SITE FOR RESIDUE XLS C 397
4
AC4
SOFTWARE
TRP D:16 , HIS D:54 , TRP D:137 , GLU D:181 , LYS D:183 , GLU D:217 , HIS D:220 , ASP D:245 , ASP D:292 , MG D:395 , HOH D:469 , HOH D:470 , HOH D:549
BINDING SITE FOR RESIDUE XLS D 397
5
AC5
SOFTWARE
GLU A:181 , GLU A:217 , ASP A:245 , ASP A:292 , XLS A:397
BINDING SITE FOR RESIDUE MG A 395
6
AC6
SOFTWARE
GLU B:181 , GLU B:217 , ASP B:245 , ASP B:292 , XLS B:397
BINDING SITE FOR RESIDUE MG B 395
7
AC7
SOFTWARE
GLU C:181 , GLU C:217 , ASP C:245 , ASP C:292 , XLS C:397
BINDING SITE FOR RESIDUE MG C 395
8
AC8
SOFTWARE
GLU D:181 , GLU D:217 , ASP D:245 , ASP D:292 , XLS D:397
BINDING SITE FOR RESIDUE MG D 395
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d5xina_ (A:)
1b: SCOP_d5xinc_ (C:)
1c: SCOP_d5xind_ (D:)
1d: SCOP_d5xinb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Xylose isomerase-like
(125)
Family
:
Xylose isomerase
(97)
Protein domain
:
D-xylose isomerase
(82)
Actinoplanes missouriensis [TaxId: 1866]
(14)
1a
d5xina_
A:
1b
d5xinc_
C:
1c
d5xind_
D:
1d
d5xinb_
B:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_5xinA00 (A:3-394)
1b: CATH_5xinB00 (B:3-394)
1c: CATH_5xinC00 (C:3-394)
1d: CATH_5xinD00 (D:3-394)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Divalent-metal-dependent TIM barrel enzymes
(98)
Actinoplanes missouriensis. Organism_taxid: 1866
(13)
1a
5xinA00
A:3-394
1b
5xinB00
B:3-394
1c
5xinC00
C:3-394
1d
5xinD00
D:3-394
[
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 (271 KB)
Header - Asym.Unit
Biol.Unit 1 (265 KB)
Header - Biol.Unit 1
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
5XIN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
