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.
1S9M
Theor. Model
Info
Theoretical Model (20 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL MODEL OF THE P170R HUMAN SOX9-DNA COMPLEX
Authors
:
S. Ranganathan, S. Mcdowall, A. Argentaro, P. Weller, S. Mertin, S. Mansour, J. Tolmie, V. Harley
Date
:
19 May 99 (Deposition) - 24 May 99 (Release) - 01 Apr 03 (Revision)
Method
:
THEORETICAL MODEL
Resolution
:
NOT APPLICABLE
Chains
:
Theor. Model : A,B,C
Keywords
:
Complex (Dna-Binding Protein/Dna)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Mcdowall, A. Argentaro, S. Ranganathan, P. Weller, S. Mertin, S. Mansour, J. Tolmie, V. Harley
Functional And Structural Studies Of Wild Type Sox9 And Mutations Causing Campomelic Dysplasia.
J. Biol. Chem. V. 274 24023 1999
(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
(15, 15)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_003735 (P8L, chain A, )
02: VAR_003736 (F12L, chain A, )
03: VAR_003737 (F12S, chain A, )
04: VAR_063643 (M13T, chain A, )
05: VAR_063644 (M13V, chain A, )
06: VAR_003738 (A19V, chain A, )
07: VAR_003739 (W43R, chain A, )
08: VAR_003740 (R52P, chain A, )
09: VAR_008529 (F54L, chain A, )
10: VAR_008530 (A58T, chain A, )
11: VAR_063645 (H65Q, chain A, )
12: VAR_008531 (H65Y, chain A, )
13: VAR_063646 (R70L, chain A, )
14: VAR_003741 (R70R, chain A, )
15: VAR_063647 (K73E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_003735
P
108
L
SOX9_HUMAN
Disease (CMD1)
---
A
P
8
L
02
UniProt
VAR_003736
F
112
L
SOX9_HUMAN
Disease (CMD1)
---
A
F
12
L
03
UniProt
VAR_003737
F
112
S
SOX9_HUMAN
Disease (CMD1)
---
A
F
12
S
04
UniProt
VAR_063643
M
113
T
SOX9_HUMAN
Disease (CMD1)
---
A
M
13
T
05
UniProt
VAR_063644
M
113
V
SOX9_HUMAN
Disease (CMD1)
---
A
M
13
V
06
UniProt
VAR_003738
A
119
V
SOX9_HUMAN
Disease (CMD1)
---
A
A
19
V
07
UniProt
VAR_003739
W
143
R
SOX9_HUMAN
Disease (CMD1)
---
A
W
43
R
08
UniProt
VAR_003740
R
152
P
SOX9_HUMAN
Disease (CMD1)
---
A
R
52
P
09
UniProt
VAR_008529
F
154
L
SOX9_HUMAN
Disease (CMD1)
---
A
F
54
L
10
UniProt
VAR_008530
A
158
T
SOX9_HUMAN
Disease (CMD1)
---
A
A
58
T
11
UniProt
VAR_063645
H
165
Q
SOX9_HUMAN
Disease (CMD1)
---
A
H
65
Q
12
UniProt
VAR_008531
H
165
Y
SOX9_HUMAN
Disease (CMD1)
28940282
A
H
65
Y
13
UniProt
VAR_063646
P
170
L
SOX9_HUMAN
Disease (CMD1)
---
A
R
70
L
14
UniProt
VAR_003741
P
170
R
SOX9_HUMAN
Disease (CMD1)
---
A
R
70
R
15
UniProt
VAR_063647
K
173
E
SOX9_HUMAN
Disease (CMD1)
---
A
K
73
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: HMG_BOX_2 (A:5-73)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HMG_BOX_2
PS50118
HMG boxes A and B DNA-binding domains profile.
SOX9_HUMAN
105-173
1
A:5-73
[
close PROSITE info
]
Exons
(2, 2)
Info
All Exons
Exon 1.1 (A:1-44)
Exon 1.2 (A:44-77)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3b
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
ENST00000245479
1
ENSE00000855029
chr17:
70117161-70117963
803
SOX9_HUMAN
1-144
144
1
A:1-44
44
1.2
ENST00000245479
2
ENSE00000855030
chr17:
70118860-70119113
254
SOX9_HUMAN
144-229
86
1
A:44-77
34
1.3b
ENST00000245479
3b
ENSE00001012847
chr17:
70119684-70122561
2878
SOX9_HUMAN
229-509
281
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 C
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:
Theoretical Model (20 KB)
Header - Theoretical Model
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
1S9M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help