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3H0A
Asym. Unit
Info
Asym.Unit (91 KB)
Biol.Unit 1 (85 KB)
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Title
:
CRYSTAL STRUCTURE OF PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA (PPARG) AND RETINOIC ACID RECEPTOR ALPHA (RXRA) IN COMPLEX WITH 9-CIS RETINOIC ACID, CO-ACTIVATOR PEPTIDE, AND A PARTIAL AGONIST
Authors
:
Z. Wang, A. Sudom, N. P. Walker
Date
:
08 Apr 09 (Deposition) - 09 Jun 09 (Release) - 02 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B,D,E (1x)
Keywords
:
Ppar, Transcription, Nuclear Receptor Fold, Transcription Regulation, Hormone, Growth Factor Receptor, Complex, Dna-Binding, Host-Virus Interaction, Isopeptide Bond, Metal-Binding, Nucleus, Receptor, Zinc-Finger, Activator, Diabetes Mellitus, Disease Mutation, Obesity, Phosphoprotein, Acyltransferase, Proto-Oncogene, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. V. Connors, Z. Wang, M. Harrison, A. Zhang, M. Wanska, S. Hiscock, B. Fox, M. Dore, M. Labelle, A. Sudom, S. Johnstone, J. Liu, N. P. Walker A. Chai, K. Siegler, Y. Li, P. Coward
Identification Of A Ppardelta Agonist With Partial Agonisti Activity On Ppargamma.
Bioorg. Med. Chem. Lett. V. 19 3550 2009
[
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 4-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,... (9RAa)
2a: [(4-{[2-(PENT-2-YN-1-YLOXY)-4-{[4-... (D30a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
9RA
1
Ligand/Ion
4-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)ETHENYL]BENZOIC ACID
2
D30
1
Ligand/Ion
[(4-{[2-(PENT-2-YN-1-YLOXY)-4-{[4-(TRIFLUOROMETHYL)PHENOXY]METHYL}PHENYL]SULFANYL}-5,6,7,8-TETRAHYDRONAPHTHALEN-1-YL)OXY]ACETIC ACID
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:117 , ILE A:268 , ALA A:271 , ALA A:272 , GLN A:275 , LEU A:309 , PHE A:313 , ARG A:316 , LEU A:326 , ALA A:327 , ILE A:345 , CYS A:432 , HIS A:435 , LEU A:436
BINDING SITE FOR RESIDUE 9RA A 500
2
AC2
SOFTWARE
HOH D:59 , HOH D:60 , HOH D:93 , HOH D:95 , LEU D:255 , GLU D:259 , ARG D:280 , ILE D:281 , GLY D:284 , CYS D:285 , ARG D:288 , ILE D:326 , LEU D:330 , LEU D:340 , GLU D:343 , LEU D:353 , MET D:364
BINDING SITE FOR RESIDUE D30 D 500
[
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SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_010725 (Q286P, chain D, )
2: VAR_010726 (R288H, chain D, )
3: VAR_010727 (V290M, chain D, )
4: VAR_050582 (A327S, chain A, )
5: VAR_014621 (S336I, chain A, )
6: VAR_022700 (F360L, chain D, )
7: VAR_022701 (R397C, chain D, )
8: VAR_050583 (A398V, chain A, )
9: VAR_010728 (P467L, chain D, )
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
D
Q
286
P
2
UniProt
VAR_010726
R
316
H
PPARG_HUMAN
Unclassified
28936407
D
R
288
H
3
UniProt
VAR_010727
V
318
M
PPARG_HUMAN
Unclassified
---
D
V
290
M
4
UniProt
VAR_050582
A
327
S
RXRA_HUMAN
Polymorphism
1805345
A
A
327
S
5
UniProt
VAR_014621
S
336
I
RXRA_HUMAN
Polymorphism
1805345
A
S
336
I
6
UniProt
VAR_022700
F
388
L
PPARG_HUMAN
Disease (FPLD3)
---
D
F
360
L
7
UniProt
VAR_022701
R
425
C
PPARG_HUMAN
Disease (FPLD3)
---
D
R
397
C
8
UniProt
VAR_050583
A
398
V
RXRA_HUMAN
Polymorphism
11542209
A
A
398
V
9
UniProt
VAR_010728
P
495
L
PPARG_HUMAN
Unclassified
---
D
P
467
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(4, 5)
Info
All Exons
Exon 1.12a (D:206-245)
Exon 1.13 (D:246-396 (gaps))
Exon 1.14e (D:396-477)
Exon 2.15a (B:629-639 | E:629-640)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.12a
2: Boundary 1.12a/1.13
3: Boundary 1.13/1.14e
4: Boundary 1.14e/-
5: Boundary 2.14/2.15a
6: Boundary 2.15a/2.16a
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
1.6a
ENST00000287820
6a
ENSE00002160702
chr3:
12392971-12393173
203
PPARG_HUMAN
1-28
28
0
-
-
1.8b
ENST00000287820
8b
ENSE00001774542
chr3:
12421203-12421430
228
PPARG_HUMAN
28-104
77
0
-
-
1.9b
ENST00000287820
9b
ENSE00001762865
chr3:
12422821-12422990
170
PPARG_HUMAN
104-160
57
0
-
-
1.10
ENST00000287820
10
ENSE00001798725
chr3:
12434113-12434251
139
PPARG_HUMAN
161-207
47
0
-
-
1.12a
ENST00000287820
12a
ENSE00001804058
chr3:
12447381-12447580
200
PPARG_HUMAN
207-273
67
1
D:206-245
40
1.13
ENST00000287820
13
ENSE00001676214
chr3:
12458203-12458653
451
PPARG_HUMAN
274-424
151
1
D:246-396 (gaps)
151
1.14e
ENST00000287820
14e
ENSE00001527068
chr3:
12475397-12475855
459
PPARG_HUMAN
424-505
82
1
D:396-477
82
2.5c
ENST00000348332
5c
ENSE00001412482
chr2:
24807346-24807429
84
NCOA1_HUMAN
-
0
0
-
-
2.6b
ENST00000348332
6b
ENSE00001353786
chr2:
24866835-24866991
157
NCOA1_HUMAN
-
0
0
-
-
2.7a
ENST00000348332
7a
ENSE00002170964
chr2:
24881530-24881635
106
NCOA1_HUMAN
1-30
30
0
-
-
2.8
ENST00000348332
8
ENSE00001070983
chr2:
24888618-24888784
167
NCOA1_HUMAN
30-86
57
0
-
-
2.9
ENST00000348332
9
ENSE00001781523
chr2:
24896235-24896332
98
NCOA1_HUMAN
86-118
33
0
-
-
2.10
ENST00000348332
10
ENSE00001796214
chr2:
24905820-24905997
178
NCOA1_HUMAN
119-178
60
0
-
-
2.11
ENST00000348332
11
ENSE00001070993
chr2:
24914350-24914529
180
NCOA1_HUMAN
178-238
61
0
-
-
2.12
ENST00000348332
12
ENSE00001070995
chr2:
24916121-24916216
96
NCOA1_HUMAN
238-270
33
0
-
-
2.13
ENST00000348332
13
ENSE00001070992
chr2:
24920527-24920667
141
NCOA1_HUMAN
270-317
48
0
-
-
2.14
ENST00000348332
14
ENSE00001071000
chr2:
24927955-24928102
148
NCOA1_HUMAN
317-366
50
0
-
-
2.15a
ENST00000348332
15a
ENSE00001070985
chr2:
24929437-24930757
1321
NCOA1_HUMAN
366-806
441
2
B:629-639
E:629-640
11
12
2.16a
ENST00000348332
16a
ENSE00000808887
chr2:
24933800-24933980
181
NCOA1_HUMAN
807-867
61
0
-
-
2.17
ENST00000348332
17
ENSE00000808888
chr2:
24949458-24949575
118
NCOA1_HUMAN
867-906
40
0
-
-
2.18
ENST00000348332
18
ENSE00000808889
chr2:
24951177-24951345
169
NCOA1_HUMAN
906-962
57
0
-
-
2.19
ENST00000348332
19
ENSE00000808890
chr2:
24952370-24952684
315
NCOA1_HUMAN
963-1067
105
0
-
-
2.20
ENST00000348332
20
ENSE00000726392
chr2:
24962301-24962402
102
NCOA1_HUMAN
1068-1101
34
0
-
-
2.21
ENST00000348332
21
ENSE00000726395
chr2:
24964653-24965055
403
NCOA1_HUMAN
1102-1236
135
0
-
-
2.22
ENST00000348332
22
ENSE00000808891
chr2:
24974851-24975025
175
NCOA1_HUMAN
1236-1294
59
0
-
-
2.23
ENST00000348332
23
ENSE00000726401
chr2:
24980842-24981025
184
NCOA1_HUMAN
1294-1355
62
0
-
-
2.24
ENST00000348332
24
ENSE00000726404
chr2:
24985556-24985645
90
NCOA1_HUMAN
1356-1385
30
0
-
-
2.26b
ENST00000348332
26b
ENSE00001797482
chr2:
24991090-24993571
2482
NCOA1_HUMAN
1386-1441
56
0
-
-
[
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SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3h0ad_ (D:)
2a: SCOP_d3h0aa_ (A:)
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Classes
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)
(
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Folds
(
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)
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(
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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
d3h0ad_
D:
Protein domain
:
Retinoid-X receptor alpha (RXR-alpha)
(36)
Human (Homo sapiens) [TaxId: 9606]
(33)
2a
d3h0aa_
A:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3h0aA00 (A:228-455)
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(
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(
)
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
3h0aA00
A:228-455
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Chain B
Chain D
Chain E
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