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Crystal structure of achbp from aplysia californica in complex with methyllycaconitine

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

PDB: 2BYR
Type: protein
Length: 2,101 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholine-binding protein
UniProt: Q8WSF8
Ligands: MLK
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 10 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholine-binding protein	protein	213	13% helix, 46% strand	Q8WSF8
B	Acetylcholine-binding protein	protein	210	11% helix, 50% strand	Q8WSF8
C	Acetylcholine-binding protein	protein	210	12% helix, 47% strand	Q8WSF8
D	Acetylcholine-binding protein	protein	211	11% helix, 52% strand	Q8WSF8
E	Acetylcholine-binding protein	protein	214	14% helix, 45% strand	Q8WSF8
F	Acetylcholine-binding protein	protein	209	8% helix, 50% strand	Q8WSF8
G	Acetylcholine-binding protein	protein	205	7% helix, 51% strand	Q8WSF8
H	Acetylcholine-binding protein	protein	204	9% helix, 50% strand	Q8WSF8
I	Acetylcholine-binding protein	protein	213	13% helix, 48% strand	Q8WSF8
J	Acetylcholine-binding protein	protein	212	13% helix, 46% strand	Q8WSF8

Ligands and binding sites

MLK · Methyllycaconitine · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I

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	1039	0.76	0.78	76	MLK
2	1001	0.75	0.78	69	MLK
3	686	0.69	0.77	67	MLK
4	710	0.69	0.77	64	MLK
5	590	0.69	0.78	47	MLK

Interfaces

13 interfaces between chains.

A–E · 1398 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 1394 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1381 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1334 Å² buried · 14 hydrogen bonds · protein-protein
F–J · 1306 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

2BYR · CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA in complex with methyllycaconitine · 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 2BYR · PDBe 2BYR · UniProt Q8WSF8

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