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.
1QBI
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (163 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS
Authors
:
A. Oubrie, H. J. Rozeboom, K. H. Kalk, J. A. Duine, B. W. Dijkstra
Date
:
22 Apr 99 (Deposition) - 25 Feb 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta-Propeller, Superbarrel, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Oubrie, H. J. Rozeboom, K. H. Kalk, J. A. Duine, B. W. Dijkstra
The 1. 7 A Crystal Structure Of The Apo Form Of The Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus Reveals A Novel Internal Conserved Sequence Repeat.
J. Mol. Biol. V. 289 319 1999
[
close entry info
]
Hetero Components
(3, 9)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: GLYCEROL (GOLa)
3a: PLATINUM (II) ION (PTa)
3b: PLATINUM (II) ION (PTb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
GOL
1
Ligand/Ion
GLYCEROL
3
PT
2
Ligand/Ion
PLATINUM (II) ION
[
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
MET B:400
BINDING SITE FOR RESIDUE PT B 462
2
AC2
SOFTWARE
GLU B:253 , TYR B:263 , HOH B:470 , HOH B:473 , HOH B:483 , HOH B:493
BINDING SITE FOR RESIDUE CA B 463
3
AC3
SOFTWARE
ALA B:269 , TYR B:271 , ASP B:273 , GLU B:309 , HOH B:480 , HOH B:999
BINDING SITE FOR RESIDUE CA B 464
4
AC4
SOFTWARE
ALA A:269 , TYR A:271 , ASP A:273 , GLU A:309 , HOH A:486 , HOH A:875
BINDING SITE FOR RESIDUE CA A 465
5
AC5
SOFTWARE
GLU A:253 , TYR A:263 , HOH A:487 , HOH A:500 , HOH A:504 , HOH A:521
BINDING SITE FOR RESIDUE CA A 466
6
AC6
SOFTWARE
GLY B:247 , PRO B:248 , HOH B:533 , HOH B:572 , HOH B:592
BINDING SITE FOR RESIDUE CA B 467
7
AC7
SOFTWARE
GLY A:247 , PRO A:248 , HOH A:520 , HOH A:664 , HOH A:672 , HOH A:870
BINDING SITE FOR RESIDUE CA A 468
8
AC8
SOFTWARE
GLN A:39 , ARG A:52 , ASN A:54 , SER A:59 , LYS A:61 , LEU B:23 , GLY B:58 , HOH B:816 , HOH B:1076
BINDING SITE FOR RESIDUE GOL A 469
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d1qbia_ (A:)
1b: SCOP_d1qbib_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
Soluble quinoprotein glucose dehydrogenase
(4)
Family
:
Soluble quinoprotein glucose dehydrogenase
(4)
Protein domain
:
Soluble quinoprotein glucose dehydrogenase
(4)
Acinetobacter calcoaceticus [TaxId: 471]
(4)
1a
d1qbia_
A:
1b
d1qbib_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1qbiA00 (A:1-450)
1b: CATH_1qbiB00 (B:1-452)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
TolB, C-terminal domain
(42)
Acinetobacter calcoaceticus. Organism_taxid: 471.
(4)
1a
1qbiA00
A:1-450
1b
1qbiB00
B:1-452
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GSDH_1qbiB01 (B:323-431)
1b: PFAM_GSDH_1qbiB02 (B:323-431)
1c: PFAM_GSDH_1qbiB03 (B:323-431)
1d: PFAM_GSDH_1qbiB04 (B:323-431)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
GSDH
(5)
Acinetobacter calcoaceticus
(1)
1a
GSDH-1qbiB01
B:323-431
1b
GSDH-1qbiB02
B:323-431
1c
GSDH-1qbiB03
B:323-431
1d
GSDH-1qbiB04
B:323-431
[
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 (169 KB)
Header - Asym.Unit
Biol.Unit 1 (163 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
1QBI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help