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Complex structure of lxr with an agonist

Analyse Complex structure of lxr 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: 3KFC
Type: protein
Length: 884 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxysterols receptor lxr-beta
UniProt: P55055
Ligands: 61X
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Oxysterols receptor lxr-beta	protein	233	72% helix, 4% strand	P55055
B	Oxysterols receptor lxr-beta	protein	232	69% helix, 2% strand	P55055
C	Oxysterols receptor lxr-beta	protein	186	69% helix, 5% strand	P55055

Ligands and binding sites

61X · 4-{3-[3-(methylsulfonyl)phenoxy]phenyl}-8-(trifluoromethyl)quinoline · ligand · 3 copies · chains A, B, D

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

Pockets

16 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	269	0.86	0.97	36	61X
2	265	0.85	0.96	37	61X
3	322	0.83	0.93	41	61X
4	350	0.75	0.85	35	empty
5	551	0.71	0.80	53	empty

Interfaces

2 interfaces between chains.

C–D · 1125 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1073 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3KFC · Complex Structure of LXR with an agonist · the same entry in another collection · chain A against A, TM-score 1.00
P55055 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-beta (P55055) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 3KFC · PDBe 3KFC · UniProt P55055

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