MolNFT v2 · #154578 · protein

Human LXR-beta in complex with a ligand

6JIO · Oxysterols receptor LXR-beta: “Human LXR-beta in complex with a ligand”. X-ray diffraction at 2.6, 1 ligand (BQ3), 10 pockets (best druggability 0.85). MolNFT v2 #154578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JIO
Type: protein
Length: 970 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.6
Source: Homo sapiens
Molecule: Oxysterols receptor LXR-beta
UniProt: P55055
Ligands: BQ3
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · resolution 2.6 · 4 distinct chains · 66% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxysterols receptor LXR-beta	protein	244	66% helix, 4% strand	P55055
B	Oxysterols receptor LXR-beta	protein	242	64% helix, 4% strand	P55055
C	Oxysterols receptor LXR-beta	protein	237	68% helix, 4% strand	P55055
D	Oxysterols receptor LXR-beta	protein	247	66% helix, 3% strand	P55055

Ligands and binding sites

BQ3 · tert-butyl 7-amino-3,4-dihydroisoquinoline-2(1H)-carboxylate · ligand · 2 copies · chains A, D

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

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	245	0.85	0.97	37	BQ3
2	235	0.85	0.97	32	BQ3
3	274	0.85	0.95	38	empty
4	241	0.84	0.96	43	empty
5	900	0.80	0.82	97	empty

Interfaces

4 interfaces between chains.

B–D · 1028 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 1008 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 55 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 36 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6JIO · Human lxr-beta in complex with a ligand · the same entry in another collection · chain D against D, TM-score 1.00
P55055 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-beta (P55055) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P55055
Elsewhere: RCSB PDB 6JIO · PDBe 6JIO · UniProt P55055

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