MolNFT v1 · #189887 · protein

An open-like conformation of the sigma-1 receptor from xenopus laevis complexed with PRE084 by co-crystallization

7W2F · Sigma non-opioid intracellular receptor 1: “An open-like conformation of the sigma-1 receptor from xenopus laevis complexed with PRE084 by…”. X-ray diffraction, 1 ligand (E84), 20 pockets (best druggability 0.83). MolNFT v1 #189887…

PDB: 7W2F
Type: protein
Length: 2,583 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sigma non-opioid intracellular receptor 1
UniProt: Q6DCU6
Ligands: E84
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F, I, J, L	Sigma non-opioid intracellular receptor 1	protein	215	43% helix, 28% strand	Q6DCU6
C	Sigma non-opioid intracellular receptor 1	protein	216	44% helix, 28% strand	Q6DCU6
G	Sigma non-opioid intracellular receptor 1	protein	219	42% helix, 28% strand	Q6DCU6
H, K	Sigma non-opioid intracellular receptor 1	protein	214	43% helix, 28% strand	Q6DCU6

Ligands and binding sites

E84 · 2-morpholin-4-ylethyl 1-phenylcyclohexane-1-carboxylate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
BOG · octyl beta-D-glucopyranoside · additive · 7 copies · chains A, B, D, E, G, I, H, J, L, K

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	291	0.83	0.94	41	E84
2	313	0.83	0.93	38	E84
3	316	0.83	0.93	42	E84
4	332	0.83	0.92	41	E84
5	329	0.83	0.92	44	E84

Interfaces

25 interfaces between chains.

B–C · 1002 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 999 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 993 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 989 Å² buried · 15 hydrogen bonds · protein-protein
H–I · 989 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7W2F · An open-like conformation of the sigma-1 receptor from Xenopus laevis complexed with… · the same entry in another collection · chain L against L, TM-score 1.00

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 Q6DCU6
Elsewhere: RCSB PDB 7W2F · PDBe 7W2F · UniProt Q6DCU6

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