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Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3920 (1-(6-bromopyridin-3-yl)-1, 4-diazepane)

Analyse Crystal structure of the acetylcholine binding protein (achbp) from lymnaea… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U8M
Type: protein
Length: 4,010 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholine-binding protein
UniProt: P58154
Ligands: 09R, SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 14 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholine-binding protein	protein	202	10% helix, 49% strand	P58154
B, G, Q, R	Acetylcholine-binding protein	protein	199	9% helix, 48% strand	P58154
C	Acetylcholine-binding protein	protein	201	10% helix, 48% strand	P58154
D	Acetylcholine-binding protein	protein	202	10% helix, 50% strand	P58154
E	Acetylcholine-binding protein	protein	196	9% helix, 49% strand	P58154
F	Acetylcholine-binding protein	protein	205	8% helix, 46% strand	P58154
H	Acetylcholine-binding protein	protein	198	9% helix, 49% strand	P58154
I	Acetylcholine-binding protein	protein	204	8% helix, 48% strand	P58154
J, N	Acetylcholine-binding protein	protein	201	10% helix, 48% strand	P58154
K	Acetylcholine-binding protein	protein	204	10% helix, 47% strand	P58154
L	Acetylcholine-binding protein	protein	203	10% helix, 49% strand	P58154
M, S, T	Acetylcholine-binding protein	protein	200	9% helix, 48% strand	P58154
O	Acetylcholine-binding protein	protein	197	9% helix, 49% strand	P58154
P	Acetylcholine-binding protein	protein	200	9% helix, 49% strand	P58154

Ligands and binding sites

09R · 1-(6-bromopyridin-3-yl)-1,4-diazepane · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
SO4 · Sulfate ion · ion · 17 copies · chains A, E, B, C, D, F, J, G, H, K, I, O, L, M, N, Q, R, S, T

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	527	0.81	0.87	71	empty
2	480	0.80	0.87	59	empty
3	381	0.80	0.89	66	empty
4	609	0.78	0.84	73	09R, SO4
5	357	0.76	0.87	50	empty

Interfaces

47 interfaces between chains.

F–G · 1433 Å² buried · 25 hydrogen bonds · protein-protein
F–J · 1430 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1422 Å² buried · 18 hydrogen bonds · protein-protein
P–T · 1417 Å² buried · 19 hydrogen bonds · protein-protein
M–N · 1415 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide (disulfide).

Compared structures

3U8M · Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in… · the same entry in another collection · chain K against K, 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 P58154
Elsewhere: RCSB PDB 3U8M · PDBe 3U8M · UniProt P58154

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