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Crystal structure of aplysia californica achbp in complex with epibatidine

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

PDB: 2BYQ
Type: protein
Length: 1,069 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble acetylcholine receptor
UniProt: Q8WSF8
Ligands: EPJ
Pockets: 20 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Soluble acetylcholine receptor	protein	214	12% helix, 50% strand	Q8WSF8
C	Soluble acetylcholine receptor	protein	214	10% helix, 50% strand	Q8WSF8
E	Soluble acetylcholine receptor	protein	213	10% helix, 50% strand	Q8WSF8

Ligands and binding sites

EPJ · Epibatidine · ligand · 5 copies · chains A, E, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.69	0.77	67	empty
2	261	0.68	0.84	43	EPJ
3	250	0.66	0.83	41	EPJ
4	226	0.65	0.83	43	EPJ
5	235	0.63	0.82	41	EPJ

Interfaces

5 interfaces between chains.

C–D · 1575 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 1557 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1523 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1496 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1482 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

2BYQ · Crystal structure of Aplysia californica AChBP in complex with epibatidine · 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 2BYQ · PDBe 2BYQ · UniProt Q8WSF8

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