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Bovine sigma-2 receptor bound to cholesterol

Analyse Bovine sigma-2 receptor bound to cholesterol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MFI
Type: protein
Length: 650 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sigma intracellular receptor 2
UniProt: Q3MHW7
Ligands: CLR
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sigma intracellular receptor 2	protein	164	74% helix, 0% strand	Q3MHW7
B	Sigma intracellular receptor 2	protein	164	77% helix, 0% strand	Q3MHW7
C	Sigma intracellular receptor 2	protein	159	77% helix, 0% strand	Q3MHW7
D	Sigma intracellular receptor 2	protein	163	75% helix, 0% strand	Q3MHW7

Ligands and binding sites

CLR · Cholesterol · ligand · 4 copies · chains A, B, C, D
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 20 copies · chains A, B, D, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C

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

Pockets

11 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	158	0.73	0.90	19	CLR
2	196	0.71	0.88	23	CLR
3	177	0.71	0.88	24	CLR
4	206	0.71	0.87	25	CLR
5	445	0.59	0.74	43	OLC

Interfaces

3 interfaces between chains.

A–B · 854 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 826 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 260 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7MFI · Bovine sigma-2 receptor bound to cholesterol · the same entry in another collection · chain D against D, TM-score 1.00
Q3MHW7 · AlphaFold monomer V2.0 prediction for sigma intracellular receptor 2 (Q3MHW7) · 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 Q3MHW7
Elsewhere: RCSB PDB 7MFI · PDBe 7MFI · UniProt Q3MHW7

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