MolNFT v1 · #90949 · protein

Crystal structure of acetylcholine binding protein (achbp) from aplysia californica in complex with alpha-conotoxin buia

4EZ1 · Soluble acetylcholine receptor: “Crystal structure of acetylcholine binding protein (achbp) from aplysia californica in complex with…”. X-ray diffraction, 2 ligands (MN, NH2), 20 pockets (best druggability 0.62). MolNFT v1 #90949 on…

PDB: 4EZ1
Type: protein
Length: 1,088 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble acetylcholine receptor; Alpha-conotoxin buia
UniProt: Q8WSF8, P69657
Ligands: MN, NH2
Pockets: 20 · best druggability 0.62

Structure

x-ray diffraction · 6 distinct chains · 12% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Soluble acetylcholine receptor	protein	203	9% helix, 51% strand	Q8WSF8
B	Soluble acetylcholine receptor	protein	203	11% helix, 48% strand	Q8WSF8
C	Soluble acetylcholine receptor	protein	207	13% helix, 46% strand	Q8WSF8
D	Soluble acetylcholine receptor	protein	208	13% helix, 48% strand	Q8WSF8
E	Soluble acetylcholine receptor	protein	202	9% helix, 52% strand	Q8WSF8
K, L, M, N, O	Alpha-conotoxin buia	protein	13	54% helix, 0% strand	P69657

Ligands and binding sites

MN · Manganese (II) ion · metal · chains C
NH2 · Amino group · ion · 5 copies · chains B, K, A, L, E, M, D, N, C, O

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

Pockets

20 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	390	0.62	0.77	52	empty
2	307	0.58	0.77	41	empty
3	298	0.55	0.76	39	empty
4	295	0.54	0.76	39	empty
5	257	0.54	0.77	37	empty

Interfaces

15 interfaces between chains.

C–D · 1338 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 1318 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1305 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1238 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 1214 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

4EZ1 · Crystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in… · the same entry in another collection · chain O against O, TM-score 1.00
P69657 · AlphaFold monomer V2.0 prediction for alpha-conotoxin buia (P69657) · a predicted model of the same protein · chain O against A, TM-score 0.46

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
Every structure of UniProt P69657
Elsewhere: RCSB PDB 4EZ1 · PDBe 4EZ1 · UniProt Q8WSF8 · UniProt P69657

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