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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: 6K9G
Type: protein
Length: 932 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxysterols receptor lxr-beta
UniProt: P55055
Ligands: D3R
Pockets: 12 · best druggability 0.85

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxysterols receptor lxr-beta	protein	249	69% helix, 4% strand	P55055
B	Oxysterols receptor lxr-beta	protein	228	71% helix, 3% strand	P55055
C	Oxysterols receptor lxr-beta	protein	225	72% helix, 4% strand	P55055
D	Oxysterols receptor lxr-beta	protein	230	70% helix, 4% strand	P55055

Ligands and binding sites

D3R · ~{tert}-butyl (2'~{R},3~{R})-2'-[3-[4-(hydroxymethyl)-3-methylsulfonyl-phenyl]phenyl]-2-oxidanylidene-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

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	309	0.85	0.94	32	D3R
2	428	0.84	0.91	48	D3R
3	460	0.84	0.91	51	D3R
4	899	0.84	0.86	104	empty
5	510	0.83	0.89	48	D3R

Interfaces

6 interfaces between chains.

B–D · 853 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 832 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 269 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 213 Å² buried · 1 hydrogen bond · protein-protein
C–D · 103 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6K9G · 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 0.96

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 6K9G · PDBe 6K9G · UniProt P55055

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