MolNFT v1 · #141245 · protein

A structure of FXR/RXR

5Z12 · Bile acid receptor: “A structure of FXR/RXR”. X-ray diffraction, 2 ligands (33Y, 9CR), 13 pockets (best druggability 0.85). MolNFT v1 #141245 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z12
Type: protein
Length: 896 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bile acid receptor; Retinoic acid receptor rxr-alpha; Peptide from nuclear receptor…
UniProt: Q96RI1, P19793
Ligands: 33Y, 9CR
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 68% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Bile acid receptor	protein	223	70% helix, 0% strand	Q96RI1
C	Retinoic acid receptor rxr-alpha	protein	203	68% helix, 3% strand	P19793
F, I	Peptide from nuclear receptor coactivator 2	protein	9	78% helix, 0% strand	—
J, H	Peptide from nuclear receptor coactivator 2	protein	6	0% helix, 0% strand	—
B	Retinoic acid receptor rxr-alpha	protein	217	66% helix, 3% strand	P19793

Ligands and binding sites

33Y · 1-methylethyl 3-[(3,4-difluorophenyl)carbonyl]-1,1-dimethyl-1,2,3,6-tetrahydroazepino[4,5-b]indole-5-carboxylate · ligand · 2 copies · chains A, D
9CR · (9cis)-retinoic acid · ligand · 2 copies · chains C, B

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	296	0.85	0.95	33	33Y
2	255	0.85	0.96	34	9CR
3	323	0.84	0.94	36	33Y
4	230	0.84	0.96	35	9CR
5	706	0.73	0.79	65	empty

Interfaces

7 interfaces between chains.

C–D · 1168 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1152 Å² buried · 10 hydrogen bonds · protein-protein
B–I · 534 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 486 Å² buried · 3 hydrogen bonds · protein-protein
D–H · 407 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5Z12 · A structure of FXR/RXR · the same entry in another collection · chain A against A, TM-score 1.00

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 Q96RI1
Every structure of UniProt P19793
Elsewhere: RCSB PDB 5Z12 · PDBe 5Z12 · UniProt Q96RI1 · UniProt P19793

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