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Human lxr-beta in complex with an agonist

Analyse Human lxr-beta in complex with an agonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K9M
Type: protein
Length: 965 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxysterols receptor lxr-beta
UniProt: P55055
Ligands: D43
Pockets: 11 · best druggability 0.86

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxysterols receptor lxr-beta	protein	242	67% helix, 4% strand	P55055
B	Oxysterols receptor lxr-beta	protein	241	66% helix, 4% strand	P55055
C	Oxysterols receptor lxr-beta	protein	237	68% helix, 4% strand	P55055
D	Oxysterols receptor lxr-beta	protein	245	67% helix, 4% strand	P55055

Ligands and binding sites

D43 · ~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-propan-2-yl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate · ligand · 4 copies · chains A, B, C, D

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

Pockets

11 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	258	0.86	0.97	27	D43
2	241	0.85	0.96	27	D43
3	281	0.84	0.94	30	D43
4	346	0.84	0.92	41	D43
5	465	0.71	0.82	57	empty

Interfaces

4 interfaces between chains.

A–C · 1013 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 962 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 97 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 38 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6K9M · Human LXR-beta in complex with an agonist · 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 D 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 6K9M · PDBe 6K9M · UniProt P55055

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