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.
1XYA
Biol. Unit 1
Info
Asym.Unit (137 KB)
Biol.Unit 1 (260 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS
Authors
:
A. Lavie, K. N. Allen, G. A. Petsko, D. Ringe
Date
:
03 Jan 94 (Deposition) - 31 May 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.81
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Isomerase(Intramolecular Oxidoreductase), Isomerase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Lavie, K. N. Allen, G. A. Petsko, D. Ringe
X-Ray Crystallographic Structures Of D-Xylose Isomerase-Substrate Complexes Position The Substrate And Provide Evidence For Metal Movement During Catalysis.
Biochemistry V. 33 5469 1994
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: HYDROXIDE ION (OHa)
2b: HYDROXIDE ION (OHb)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: M1A (AUTHOR)
08: M1B (AUTHOR)
09: M2A (AUTHOR)
10: M2B (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:180 , GLU A:216 , ASP A:244 , ASP A:286
BINDING SITE FOR RESIDUE MG A 400
02
AC2
SOFTWARE
GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , OH A:1700
BINDING SITE FOR RESIDUE MG A 401
03
AC3
SOFTWARE
GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , MG A:401 , HOH A:1415
BINDING SITE FOR RESIDUE OH A 1700
04
AC4
SOFTWARE
GLU B:680 , GLU B:716 , ASP B:744 , ASP B:786
BINDING SITE FOR RESIDUE MG B 900
05
AC5
SOFTWARE
GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , OH B:1800
BINDING SITE FOR RESIDUE MG B 901
06
AC6
SOFTWARE
GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , ASP B:786 , MG B:901 , HOH B:1354
BINDING SITE FOR RESIDUE OH B 1800
07
M1A
AUTHOR
MG A:400 , GLU A:180 , ASP A:244 , ASP A:286 , GLU A:216
METAL BINDING SITE
08
M1B
AUTHOR
MG B:900 , GLU B:680 , ASP B:744 , ASP B:786 , GLU B:716
METAL BINDING SITE
09
M2A
AUTHOR
MG A:401 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , OH A:1700
METAL BINDING SITE
10
M2B
AUTHOR
MG B:901 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , OH B:1800
METAL BINDING SITE
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: XYLOSE_ISOMERASE (A:3-382,B:503-882)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
XYLOSE_ISOMERASE
PS51415
Xylose isomerase family profile.
XYLA_STROL
4-383
4
A:3-382
B:503-882
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1xyaa_ (A:)
1b: SCOP_d1xyab_ (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)
Streptomyces olivochromogenes [TaxId: 1963]
(9)
1a
d1xyaa_
A:
1b
d1xyab_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1xyaA00 (A:1-386)
1b: CATH_1xyaB00 (B:501-886)
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)
Streptomyces olivochromogenes. Organism_taxid: 1963
(6)
1a
1xyaA00
A:1-386
1b
1xyaB00
B:501-886
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_AP_endonuc_2_1xyaB01 (B:539-764)
1b: PFAM_AP_endonuc_2_1xyaB02 (B:539-764)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
AP_endonuc_2
(72)
Streptomyces olivochromogenes
(8)
1a
AP_endonuc_2-1xyaB01
B:539-764
1b
AP_endonuc_2-1xyaB02
B:539-764
[
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
Asymmetric Unit 2
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 (137 KB)
Header - Asym.Unit
Biol.Unit 1 (260 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
1XYA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help