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.
3B1M
Asym. Unit
Info
Asym.Unit (55 KB)
Biol.Unit 1 (51 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 PPARGAMMA-LBD COMPLEXED WITH A CERCOSPORAMIDE DERIVATIVE MODULATOR CERCO-A
Authors
:
Y. Matsui, H. Hiroyuki
Date
:
05 Jul 11 (Deposition) - 24 Aug 11 (Release) - 24 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transcription
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Wakabayashi, S. Hayashi, Y. Matsui, T. Matsumoto, A. Furukawa, M. Kuroha, N. Tanaka, T. Inaba, S. Kanda, J. Tanaka, R. Okuyama, S. Wakimoto, T. Ogata, K. Araki, J. Ohsumi
Pharmacology And In Vitro Profiling Of A Novel Peroxisome Proliferator-Activated Receptor Gamma Ligand, Cerco-A
Biol. Pharm. Bull. V. 34 1094 2011
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: (9AS)-8-ACETYL-N-[(2-ETHYLNAPHTHAL... (KRCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
KRC
1
Ligand/Ion
(9AS)-8-ACETYL-N-[(2-ETHYLNAPHTHALEN-1-YL)METHYL]-1,7-DIHYDROXY-3-METHOXY-9A-METHYL-9-OXO-9,9A-DIHYDRODIBENZO[B,D]FURAN-4-CARBOXAMIDE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:38 , HOH A:53 , ILE A:262 , GLY A:284 , CYS A:285 , PHE A:287 , ARG A:288 , SER A:289 , LEU A:330 , MET A:334 , ILE A:341 , SER A:342 , LEU A:353 , LYS A:367 , HOH A:490
BINDING SITE FOR RESIDUE KRC A 1
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_010725 (Q286P, chain A, )
2: VAR_010726 (R288H, chain A, )
3: VAR_010727 (V290M, chain A, )
4: VAR_022700 (F360L, chain A, )
5: VAR_022701 (R397C, chain A, )
6: VAR_010728 (P467L, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_010725
Q
314
P
PPARG_HUMAN
Unclassified
28936407
A
Q
286
P
2
UniProt
VAR_010726
R
316
H
PPARG_HUMAN
Unclassified
28936407
A
R
288
H
3
UniProt
VAR_010727
V
318
M
PPARG_HUMAN
Unclassified
---
A
V
290
M
4
UniProt
VAR_022700
F
388
L
PPARG_HUMAN
Disease (FPLD3)
---
A
F
360
L
5
UniProt
VAR_022701
R
425
C
PPARG_HUMAN
Disease (FPLD3)
---
A
R
397
C
6
UniProt
VAR_010728
P
495
L
PPARG_HUMAN
Unclassified
---
A
P
467
L
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
(5, 5)
Info
All Exons
Exon 1.12b (B:6-8)
Exon 1.13b (B:9-16)
Exon 2.12a (A:206-245)
Exon 2.13 (A:246-396 (gaps))
Exon 2.14e (A:396-477)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5a/1.12b
2: Boundary 1.12b/1.13b
3: Boundary 1.13b/1.14c
4: Boundary 2.10/2.12a
5: Boundary 2.12a/2.13
6: Boundary 2.13/2.14e
7: Boundary 2.14e/-
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
1.4a
ENST00000264867
4a
ENSE00001267865
chr4:
23891700-23891527
174
PRGC1_HUMAN
1-18
18
0
-
-
1.5a
ENST00000264867
5a
ENSE00001008295
chr4:
23886554-23886375
180
PRGC1_HUMAN
19-78
60
0
-
-
1.12b
ENST00000264867
12b
ENSE00000969448
chr4:
23833374-23833180
195
PRGC1_HUMAN
79-143
65
1
B:6-8
3
1.13b
ENST00000264867
13b
ENSE00000969449
chr4:
23831208-23831086
123
PRGC1_HUMAN
144-184
41
1
B:9-16
8
1.14c
ENST00000264867
14c
ENSE00000969450
chr4:
23830227-23830023
205
PRGC1_HUMAN
185-253
69
0
-
-
1.16
ENST00000264867
16
ENSE00000969451
chr4:
23826131-23826086
46
PRGC1_HUMAN
253-268
16
0
-
-
1.17b
ENST00000264867
17b
ENSE00000969452
chr4:
23825976-23825903
74
PRGC1_HUMAN
268-293
26
0
-
-
1.19c
ENST00000264867
19c
ENSE00000969453
chr4:
23816228-23815313
916
PRGC1_HUMAN
293-598
306
0
-
-
1.20
ENST00000264867
20
ENSE00000969454
chr4:
23814748-23814644
105
PRGC1_HUMAN
598-633
36
0
-
-
1.21
ENST00000264867
21
ENSE00000969455
chr4:
23814490-23814370
121
PRGC1_HUMAN
633-673
41
0
-
-
1.22
ENST00000264867
22
ENSE00000969456
chr4:
23803968-23803847
122
PRGC1_HUMAN
674-714
41
0
-
-
1.23
ENST00000264867
23
ENSE00000969457
chr4:
23803504-23803353
152
PRGC1_HUMAN
714-765
52
0
-
-
1.24c
ENST00000264867
24c
ENSE00001490990
chr4:
23797548-23793644
3905
PRGC1_HUMAN
765-798
34
0
-
-
2.6a
ENST00000287820
6a
ENSE00002160702
chr3:
12392971-12393173
203
PPARG_HUMAN
1-28
28
0
-
-
2.8b
ENST00000287820
8b
ENSE00001774542
chr3:
12421203-12421430
228
PPARG_HUMAN
28-104
77
0
-
-
2.9b
ENST00000287820
9b
ENSE00001762865
chr3:
12422821-12422990
170
PPARG_HUMAN
104-160
57
0
-
-
2.10
ENST00000287820
10
ENSE00001798725
chr3:
12434113-12434251
139
PPARG_HUMAN
161-207
47
0
-
-
2.12a
ENST00000287820
12a
ENSE00001804058
chr3:
12447381-12447580
200
PPARG_HUMAN
207-273
67
1
A:206-245
40
2.13
ENST00000287820
13
ENSE00001676214
chr3:
12458203-12458653
451
PPARG_HUMAN
274-424
151
1
A:246-396 (gaps)
151
2.14e
ENST00000287820
14e
ENSE00001527068
chr3:
12475397-12475855
459
PPARG_HUMAN
424-505
82
1
A:396-477
82
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3b1ma_ (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
:
Peroxisome proliferator activated receptor gamma, PPAR-gamma
(83)
Human (Homo sapiens) [TaxId: 9606]
(83)
1a
d3b1ma_
A:
[
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
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 (55 KB)
Header - Asym.Unit
Biol.Unit 1 (51 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
3B1M
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
