MolNFT v1 · #30875 · protein

Liver X-receptor alpha ligand binding domain with SB313987

2ACL · Retinoic acid receptor rxr-alpha: “Liver X-receptor alpha ligand binding domain with SB313987”. X-ray diffraction, 2 ligands (REA, L05), 20 pockets (best druggability 0.85). MolNFT v1 #30875 on GenesisL1: 3D structure, binding sites…

PDB: 2ACL
Type: protein
Length: 1,827 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoic acid receptor rxr-alpha; Oxysterols receptor lxr-alpha
UniProt: P19793, Q9Z0Y9
Ligands: REA, L05
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, G	Retinoic acid receptor rxr-alpha	protein	214	68% helix, 3% strand	P19793
B, D, F	Oxysterols receptor lxr-alpha	protein	242	67% helix, 3% strand	Q9Z0Y9
C	Retinoic acid receptor rxr-alpha	protein	215	67% helix, 3% strand	P19793
H	Oxysterols receptor lxr-alpha	protein	244	64% helix, 4% strand	Q9Z0Y9

Ligands and binding sites

REA · Retinoic acid · ligand · 4 copies · chains A, E, C, G
L05 · 1-benzyl-3-(4-methoxyphenylamino)-4-phenylpyrrole-2,5-dione · ligand · 4 copies · chains B, D, F, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	300	0.85	0.95	38	L05
2	289	0.85	0.95	34	L05
3	244	0.85	0.96	28	REA
4	297	0.84	0.94	36	L05
5	351	0.83	0.92	41	REA

Interfaces

13 interfaces between chains.

G–H · 1983 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1808 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1709 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1697 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 902 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2ACL · Liver X-Receptor alpha Ligand Binding Domain with SB313987 · the same entry in another collection · chain H against H, TM-score 1.00
Q9Z0Y9 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-alpha (Q9Z0Y9) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9Z0Y9
Elsewhere: RCSB PDB 2ACL · PDBe 2ACL · UniProt P19793 · UniProt Q9Z0Y9

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