MolNFT v1 · #146522 · protein

Human sigma-1 receptor bound to ne-100

6DK0 · Sigma non-opioid intracellular receptor 1: “Human sigma-1 receptor bound to ne-100”. X-ray diffraction, 2 ligands (GKY, SO4), 7 pockets (best druggability 0.84). MolNFT v1 #146522 on GenesisL1: 3D structure, binding sites and…

PDB: 6DK0
Type: protein
Length: 652 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sigma non-opioid intracellular receptor 1
UniProt: Q99720
Ligands: GKY, SO4
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sigma non-opioid intracellular receptor 1	protein	212	42% helix, 30% strand	Q99720
B	Sigma non-opioid intracellular receptor 1	protein	220	39% helix, 28% strand	Q99720
C	Sigma non-opioid intracellular receptor 1	protein	220	40% helix, 28% strand	Q99720

Ligands and binding sites

GKY · N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 8 copies · chains A, C
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	226	0.84	0.96	33	GKY
2	285	0.83	0.94	43	GKY
3	285	0.83	0.94	43	GKY
4	162	0.78	0.95	60	SO4
5	156	0.44	0.75	20	empty

Interfaces

3 interfaces between chains.

A–C · 1023 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1017 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 968 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6DK0 · Human sigma-1 receptor bound to NE-100 · the same entry in another collection · chain A against A, TM-score 1.00
Q99720 · AlphaFold monomer V2.0 prediction for sigma non-opioid intracellular receptor 1 (Q99720) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q99720
Elsewhere: RCSB PDB 6DK0 · PDBe 6DK0 · UniProt Q99720

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