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Co-crystal structure of ac-achbpp in complex with [N9A]LVIA

Analyse Co-crystal structure of ac-achbpp in complex with [N9A]LVIA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M4X
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 lvia
UniProt: Q8WSF8, L8BU87
Ligands: NH2
Pockets: 20 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, G, I	Soluble acetylcholine receptor	protein	207	9% helix, 53% strand	Q8WSF8
F, C, E, H, J	Alpha-conotoxin lvia	protein	16	44% helix, 0% strand	L8BU87

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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.65	0.76	54	empty
2	492	0.63	0.76	58	empty
3	415	0.62	0.77	47	empty
4	242	0.62	0.81	35	empty
5	405	0.61	0.76	46	empty

Interfaces

15 interfaces between chains.

A–B · 1221 Å² buried · 17 hydrogen bonds · protein-protein
D–I · 1216 Å² buried · 14 hydrogen bonds · protein-protein
G–I · 1195 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1190 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 1171 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

6M4X · Co-crystal structure of Ac-AChBPP in complex with [N9A]LvIA · the same entry in another collection · chain J against J, TM-score 1.00
L8BU87 · AlphaFold monomer V2.0 prediction for alpha-conotoxin lvia (L8BU87) · a predicted model of the same protein · chain E against A, TM-score 0.63

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 L8BU87
Elsewhere: RCSB PDB 6M4X · PDBe 6M4X · UniProt Q8WSF8 · UniProt L8BU87

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