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.
1S0Z
Asym. Unit
Info
Asym.Unit (48 KB)
Biol.Unit 1 (45 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 VDR LBD COMPLEXED TO SEOCALCITOL.
Authors
:
G. Tocchini-Valentini, N. Rochel, J. M. Wurtz, D. Moras
Date
:
05 Jan 04 (Deposition) - 13 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Nuclear Receptor, Transcription Regulation, Alpha-Helical Sandwich, Gene Regulation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Tocchini-Valentini, N. Rochel, J. M. Wurtz, D. Moras
Crystal Structures Of The Vitamin D Nuclear Receptor Liganded With The Vitamin D Side Chain Analogues Calcipotriol And Seocalcitol, Receptor Agonists Of Clinical Importance. Insights Into A Structural Basis For The Switching Of Calcipotriol To A Receptor Antagonist By Further Side Chain Modification.
J. Med. Chem. V. 47 1956 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: SEOCALCITOL (EB1a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EB1
1
Ligand/Ion
SEOCALCITOL
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:143 , LEU A:227 , ALA A:231 , LEU A:233 , SER A:237 , ILE A:271 , ARG A:274 , SER A:275 , SER A:278 , TRP A:286 , CYS A:288 , HIS A:305 , LEU A:309 , HIS A:397 , LEU A:414 , PHE A:422
BINDING SITE FOR RESIDUE EB1 A 510
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_029309 (L230V, chain A, )
2: VAR_004664 (R274L, chain A, )
3: VAR_004665 (H305Q, chain A, )
4: VAR_004666 (I314S, chain A, )
5: VAR_029310 (T362I, chain A, )
6: VAR_004667 (R391C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_029309
L
230
V
VDR_HUMAN
Polymorphism
11574090
A
L
230
V
2
UniProt
VAR_004664
R
274
L
VDR_HUMAN
Disease (VDDR2A)
---
A
R
274
L
3
UniProt
VAR_004665
H
305
Q
VDR_HUMAN
Disease (VDDR2A)
---
A
H
305
Q
4
UniProt
VAR_004666
I
314
S
VDR_HUMAN
Disease (VDDR2A)
---
A
I
314
S
5
UniProt
VAR_029310
T
362
I
VDR_HUMAN
Polymorphism
11574115
A
T
362
I
6
UniProt
VAR_004667
R
391
C
VDR_HUMAN
Disease (VDDR2A)
---
A
R
391
C
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
(6, 6)
Info
All Exons
Exon 1.6 (A:120-154)
Exon 1.7 (A:155-164)
Exon 1.8 (A:216-252)
Exon 1.9 (A:252-303)
Exon 1.10 (A:303-342)
Exon 1.11 (A:342-423)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5/1.6
2: Boundary 1.6/1.7
3: Boundary 1.7/1.8
4: Boundary 1.8/1.9
5: Boundary 1.9/1.10
6: Boundary 1.10/1.11
7: Boundary 1.11/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000395324
1
ENSE00001485612
chr12:
48298814-48298738
77
VDR_HUMAN
-
0
0
-
-
1.3
ENST00000395324
3
ENSE00001354497
chr12:
48276557-48276477
81
VDR_HUMAN
-
0
0
-
-
1.4
ENST00000395324
4
ENSE00000888048
chr12:
48272898-48272751
148
VDR_HUMAN
1-49
49
0
-
-
1.5
ENST00000395324
5
ENSE00000738168
chr12:
48258960-48258830
131
VDR_HUMAN
49-93
45
0
-
-
1.6
ENST00000395324
6
ENSE00000738167
chr12:
48251471-48251287
185
VDR_HUMAN
93-154
62
1
A:120-154
35
1.7
ENST00000395324
7
ENSE00000738166
chr12:
48251032-48250912
121
VDR_HUMAN
155-195
41
1
A:155-164
10
1.8
ENST00000395324
8
ENSE00000738165
chr12:
48249584-48249413
172
VDR_HUMAN
195-252
58
1
A:216-252
37
1.9
ENST00000395324
9
ENSE00000738164
chr12:
48240591-48240440
152
VDR_HUMAN
252-303
52
1
A:252-303
52
1.10
ENST00000395324
10
ENSE00000738163
chr12:
48240234-48240118
117
VDR_HUMAN
303-342
40
1
A:303-342
40
1.11
ENST00000395324
11
ENSE00001419012
chr12:
48238788-48235322
3467
VDR_HUMAN
342-427
86
1
A:342-423
82
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1s0za_ (A:)
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
:
Vitamin D nuclear receptor
(37)
Human (Homo sapiens) [TaxId: 9606]
(22)
1a
d1s0za_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1s0zA00 (A:120-423)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Retinoid X Receptor
(409)
Homologous Superfamily
:
Retinoid X Receptor
(409)
Human (Homo sapiens)
(337)
1a
1s0zA00
A:120-423
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Hormone_recep_1s0zA01 (A:216-418)
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-1s0zA01
A:216-418
[
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
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 (48 KB)
Header - Asym.Unit
Biol.Unit 1 (45 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
1S0Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
