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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2ZY0
Asym. Unit
Info
Asym.Unit (80 KB)
Biol.Unit 1 (74 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 THE HUMAN RXR ALPHA LIGAND BINDING DOMAIN BOUND TO A SYNTHETIC AGONIST COMPOUND AND A COACTIVATOR PEPTIDE
Authors
:
Y. Sato, P. Antony, N. Rochel, D. Moras, Structural Genomics Consortium For Research On Gene Expression (Sgcges)
Date
:
09 Jan 09 (Deposition) - 11 Aug 09 (Release) - 11 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transcription Regulation, Nuclear Receptor, Structural Genomics, Structural Genomics Consortium For Research On Gene Expression, Sgcges
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. P. Lippert, C. Burschka, K. Gotz, M. Kaupp, D. Ivanova, C. Gaudon, Y. Sato, P. Antony, N. Rochel, D. Moras, H. Gronemeyer, R. Tacke
Silicon Analogues Of The Rxr-Selective Retinoid Agonist Sr11237 (Bms649): Chemistry And Biology
Chemmedchem V. 4 1143 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: 4-[2-(1,1,3,3-TETRAMETHYL-2,3-DIHY... (21Pa)
1b: 4-[2-(1,1,3,3-TETRAMETHYL-2,3-DIHY... (21Pb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
21P
2
Ligand/Ion
4-[2-(1,1,3,3-TETRAMETHYL-2,3-DIHYDRO-1H-1,3-BENZODISILOL-5-YL)-1,3-DIOXOLAN-2-YL]BENZOIC ACID
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:268 , ALA A:271 , ALA A:272 , GLN A:275 , TRP A:305 , ASN A:306 , LEU A:309 , ILE A:310 , PHE A:313 , ARG A:316 , ILE A:324 , LEU A:326 , ALA A:327 , CYS A:432 , HIS A:435
BINDING SITE FOR RESIDUE 21P A 1
2
AC2
SOFTWARE
ILE C:268 , ALA C:271 , ALA C:272 , GLN C:275 , ASN C:306 , LEU C:309 , ILE C:310 , PHE C:313 , ARG C:316 , ALA C:327 , VAL C:349 , CYS C:432 , HIS C:435
BINDING SITE FOR RESIDUE 21P C 2
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_050582 (A327S, chain A/C, )
2: VAR_014621 (S336I, chain A/C, )
3: VAR_050583 (A398V, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_050582
A
327
S
RXRA_HUMAN
Polymorphism
1805345
A/C
A
327
S
2
UniProt
VAR_014621
S
336
I
RXRA_HUMAN
Polymorphism
1805345
A/C
S
336
I
3
UniProt
VAR_050583
A
398
V
RXRA_HUMAN
Polymorphism
11542209
A/C
A
398
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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_d2zy0a_ (A:)
1b: SCOP_d2zy0c_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Nuclear receptor ligand-binding domain
(609)
Superfamily
:
Nuclear receptor ligand-binding domain
(609)
Family
:
Nuclear receptor ligand-binding domain
(598)
Protein domain
:
Retinoid-X receptor alpha (RXR-alpha)
(36)
Human (Homo sapiens) [TaxId: 9606]
(33)
1a
d2zy0a_
A:
1b
d2zy0c_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Hormone_recep_2zy0C01 (C:262-442)
1b: PFAM_Hormone_recep_2zy0C02 (C:262-442)
2a: PFAM_SRC_1_2zy0D01 (D:471-481)
2b: PFAM_SRC_1_2zy0D02 (D:471-481)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Hormone_recep]
(290)
Family
:
Hormone_recep
(290)
Homo sapiens (Human)
(244)
1a
Hormone_recep-2zy0C01
C:262-442
1b
Hormone_recep-2zy0C02
C:262-442
Clan
:
no clan defined [family: SRC-1]
(47)
Family
:
SRC-1
(47)
Homo sapiens (Human)
(33)
2a
SRC-1-2zy0D01
D:471-481
2b
SRC-1-2zy0D02
D:471-481
[
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 (80 KB)
Header - Asym.Unit
Biol.Unit 1 (74 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
2ZY0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help