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The 2.3 ångström resolution crystal structure of the heterodimer of the human ppargamma and rxralpha ligand binding domains respectively bound with GW409544 and 9-cis retinoic acid and co-activator peptides.

Analyse The 2.3 ångström resolution crystal structure of the heterodimer of the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1K74
Type: protein
Length: 530 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor rxr-alpha; Peroxisome proliferator activated receptor gamma…
UniProt: P19793, P37231, O43792
Ligands: 9CR, 544
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoic acid receptor rxr-alpha	protein	232	61% helix, 3% strand	P19793
D	Peroxisome proliferator activated receptor gamma	protein	272	64% helix, 5% strand	P37231
B	Steroid receptor coactivator	protein	10	70% helix, 0% strand	O43792
E	Steroid receptor coactivator	protein	16	50% helix, 0% strand	O43792

Ligands and binding sites

9CR · (9cis)-retinoic acid · ligand · chains A
544 · 2-(1-methyl-3-oxo-3-phenyl-propylamino)-3-{4-[2-(5-methyl-2-phenyl-oxazol-4-yl)-ethoxy]-phenyl}-propionic acid · ligand · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	662	0.84	0.88	71	544
2	317	0.84	0.93	44	9CR
3	397	0.66	0.80	39	empty
4	136	0.45	0.77	20	empty
5	91	0.40	0.77	25	empty

Interfaces

3 interfaces between chains.

A–D · 1203 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 653 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 555 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1K74 · The 2.3 Angstrom resolution crystal structure of the heterodimer of the human PPARgamma… · the same entry in another collection · chain A against A, TM-score 1.00
P37231 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain D against A, TM-score 0.96
P19793 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P19793) · a predicted model of the same protein · chain A against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P19793
Every structure of UniProt P37231
Every structure of UniProt O43792
Elsewhere: RCSB PDB 1K74 · PDBe 1K74 · UniProt P19793 · UniProt P37231 · UniProt O43792

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