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.
1IZ1
Asym. Unit
Info
Asym.Unit (187 KB)
Biol.Unit 1 (182 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 CBNR, A LYSR FAMILY TRANSCRIPTIONAL REGULATOR
Authors
:
S. Muraoka, R. Okumura, N. Ogawa, K. Miyashita, T. Senda
Date
:
18 Sep 02 (Deposition) - 06 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,P,Q
Biol. Unit 1: A,B,P,Q (1x)
Keywords
:
Long Alpha Helix Connecting Dna Binding And Regulatory Domains, Dna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Muraoka, R. Okumura, N. Ogawa, T. Nonaka, K. Miyashita, T. Senda
Crystal Structure Of A Full-Length Lysr-Type Transcriptional Regulator, Cbnr: Unusual Combination Of Two Subunit Forms And Molecular Bases For Causing And Changing Dna Bend
J. Mol. Biol. V. 328 555 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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_d1iz1a1 (A:1-89)
1b: SCOP_d1iz1b1 (B:1-89)
1c: SCOP_d1iz1p1 (P:1-89)
1d: SCOP_d1iz1q1 (Q:1-89)
2a: SCOP_d1iz1a2 (A:90-292)
2b: SCOP_d1iz1b2 (B:90-294)
2c: SCOP_d1iz1p2 (P:90-292)
2d: SCOP_d1iz1q2 (Q:90-292)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
LysR-like transcriptional regulators
(3)
Protein domain
:
LysR-type regulatory protein CbnR
(2)
Ralstonia eutropha [TaxId: 106590]
(2)
1a
d1iz1a1
A:1-89
1b
d1iz1b1
B:1-89
1c
d1iz1p1
P:1-89
1d
d1iz1q1
Q:1-89
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
LysR-type regulatory protein CbnR
(2)
Ralstonia eutropha [TaxId: 106590]
(2)
2a
d1iz1a2
A:90-292
2b
d1iz1b2
B:90-294
2c
d1iz1p2
P:90-292
2d
d1iz1q2
Q:90-292
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1iz1A03 (A:162-267)
1b: CATH_1iz1B03 (B:162-267)
1c: CATH_1iz1P03 (P:162-267)
1d: CATH_1iz1Q03 (Q:162-267)
1e: CATH_1iz1B02 (B:88-161,B:268-293)
1f: CATH_1iz1A02 (A:88-161,A:268-292)
1g: CATH_1iz1P02 (P:88-161,P:268-292)
1h: CATH_1iz1Q02 (Q:88-161,Q:268-292)
2a: CATH_1iz1B01 (B:7-87)
2b: CATH_1iz1Q01 (Q:7-87)
2c: CATH_1iz1A01 (A:2-87)
2d: CATH_1iz1P01 (P:2-87)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Cupriavidus necator. Organism_taxid: 106590.
(1)
1a
1iz1A03
A:162-267
1b
1iz1B03
B:162-267
1c
1iz1P03
P:162-267
1d
1iz1Q03
Q:162-267
1e
1iz1B02
B:88-161,B:268-293
1f
1iz1A02
A:88-161,A:268-292
1g
1iz1P02
P:88-161,P:268-292
1h
1iz1Q02
Q:88-161,Q:268-292
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
Cupriavidus necator. Organism_taxid: 106590.
(1)
2a
1iz1B01
B:7-87
2b
1iz1Q01
Q:7-87
2c
1iz1A01
A:2-87
2d
1iz1P01
P:2-87
[
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 P
Chain Q
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 (187 KB)
Header - Asym.Unit
Biol.Unit 1 (182 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
1IZ1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
