MolNFT v1 · #53204 · protein

Crystal structure of aplysia achbp in complex with anabaseine

2WNL · Soluble acetylcholine receptor: “Crystal structure of aplysia achbp in complex with anabaseine”. X-ray diffraction, 4 ligands (AN4, AN5, NAG), 20 pockets (best druggability 0.76). MolNFT v1 #53204 on GenesisL1: 3D structure, binding…

PDB: 2WNL
Type: protein
Length: 2,115 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble acetylcholine receptor
UniProt: Q8WSF8
Ligands: AN4, AN5, NAG, MG
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 11% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Soluble acetylcholine receptor	protein	213	8% helix, 48% strand	Q8WSF8
B	Soluble acetylcholine receptor	protein	211	13% helix, 46% strand	Q8WSF8
C	Soluble acetylcholine receptor	protein	209	12% helix, 49% strand	Q8WSF8
D, J	Soluble acetylcholine receptor	protein	212	11% helix, 50% strand	Q8WSF8
E	Soluble acetylcholine receptor	protein	214	12% helix, 48% strand	Q8WSF8
F, I	Soluble acetylcholine receptor	protein	211	10% helix, 52% strand	Q8WSF8
G	Soluble acetylcholine receptor	protein	210	12% helix, 49% strand	Q8WSF8
H	Soluble acetylcholine receptor	protein	212	13% helix, 48% strand	Q8WSF8

Ligands and binding sites

AN4 · 3,4,5,6-tetrahydro-2,3'-bipyridine · ligand · 5 copies · chains A, E, B, D, F, G, I, J
AN5 · 5-amino-1-pyridin-3-ylpentan-1-one · ligand · 4 copies · chains A, E, C, D, F, J, H, I
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, E, F, G, H
MG · Magnesium ion · metal · 3 copies · chains C, H, E
PG4 · Tetraethylene glycol · additive · chains B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	763	0.76	0.80	72	AN4
2	316	0.73	0.86	54	AN4
3	853	0.71	0.76	87	AN5
4	555	0.69	0.78	52	empty
5	548	0.68	0.78	61	PG4

Interfaces

12 interfaces between chains.

F–G · 1536 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1453 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1414 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1376 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 1370 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

2WNL · Crystal structure of aplysia achbp in complex with anabaseine · the same entry in another collection · chain A against A, 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 Q8WSF8
Elsewhere: RCSB PDB 2WNL · PDBe 2WNL · UniProt Q8WSF8

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