MolNFT v1 · #181886 · protein

Bovine sigma-2 receptor bound to PB28

7M93 · Sigma intracellular receptor 2: “Bovine sigma-2 receptor bound to PB28”. X-ray diffraction, 1 ligand (YT1), 12 pockets (best druggability 0.73). MolNFT v1 #181886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7M93
Type: protein
Length: 652 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sigma intracellular receptor 2
UniProt: Q3MHW7
Ligands: YT1
Pockets: 12 · 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	165	75% helix, 0% strand	Q3MHW7
B	Sigma intracellular receptor 2	protein	165	77% helix, 0% strand	Q3MHW7
C	Sigma intracellular receptor 2	protein	159	77% helix, 0% strand	Q3MHW7
D	Sigma intracellular receptor 2	protein	163	76% helix, 0% strand	Q3MHW7

Ligands and binding sites

YT1 · PB28 · ligand · 4 copies · chains A, B, C, D
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 13 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.73	0.92	19	YT1
2	150	0.71	0.89	21	YT1
3	167	0.70	0.88	23	YT1
4	159	0.70	0.88	22	YT1
5	273	0.52	0.74	32	OLC

Interfaces

4 interfaces between chains.

A–B · 890 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 824 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 396 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 34 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7M93 · Bovine sigma-2 receptor bound to PB28 · 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 D 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 7M93 · PDBe 7M93 · UniProt Q3MHW7

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