Research workbench

Crystal structure of ac-achbp in complex with conotoxin gic

Analyse Crystal structure of ac-achbp in complex with conotoxin gic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CO5
Type: protein
Length: 1,115 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble acetylcholine receptor; Alpha-conotoxin gic
UniProt: Q8WSF8, Q86RB2
Ligands: NH2
Pockets: 20 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, G, I	Soluble acetylcholine receptor	protein	207	9% helix, 50% strand	Q8WSF8
F, C, E, H, J	Alpha-conotoxin gic	protein	16	56% helix, 0% strand	Q86RB2

Ligands and binding sites

NH2 · Amino group · ion · 5 copies · chains F, G, A, C, B, E, H, I, D, J

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	400	0.62	0.77	47	empty
2	405	0.60	0.76	46	empty
3	372	0.60	0.77	46	empty
4	360	0.60	0.77	39	empty
5	338	0.58	0.76	39	empty

Interfaces

15 interfaces between chains.

A–B · 1239 Å² buried · 10 hydrogen bonds · protein-protein
G–I · 1226 Å² buried · 10 hydrogen bonds · protein-protein
D–I · 1218 Å² buried · 13 hydrogen bonds · protein-protein
A–G · 1208 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 1184 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

5CO5 · Crystal structure of Ac-AChBP in complex with conotoxin GIC · the same entry in another collection · chain J against J, TM-score 1.00
Q86RB2 · AlphaFold monomer V2.0 prediction for alpha-conotoxin gic (Q86RB2) · a predicted model of the same protein · chain E against A, TM-score 0.78

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 Q86RB2
Elsewhere: RCSB PDB 5CO5 · PDBe 5CO5 · UniProt Q8WSF8 · UniProt Q86RB2

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