MolNFT v1 · #80823 · protein

Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3573 (1-(5-ethoxypyridin-3-yl)-1, 4-diazepane)

3U8K · Acetylcholine-binding protein: “Crystal structure of the acetylcholine binding protein (achbp) from lymnaea stagnalis in complex with NS3573…”. X-ray diffraction, 3 ligands (09P, NAG, SO4), 20 pockets (best druggability 0.76).…

PDB: 3U8K
Type: protein
Length: 4,043 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholine-binding protein
UniProt: P58154
Ligands: 09P, NAG, SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 19 distinct chains · 8% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholine-binding protein	protein	209	8% helix, 46% strand	P58154
B, P	Acetylcholine-binding protein	protein	200	8% helix, 50% strand	P58154
C	Acetylcholine-binding protein	protein	203	8% helix, 47% strand	P58154
D	Acetylcholine-binding protein	protein	203	8% helix, 47% strand	P58154
E	Acetylcholine-binding protein	protein	201	8% helix, 47% strand	P58154
F	Acetylcholine-binding protein	protein	203	8% helix, 46% strand	P58154
G	Acetylcholine-binding protein	protein	200	9% helix, 47% strand	P58154
H	Acetylcholine-binding protein	protein	208	8% helix, 45% strand	P58154
I	Acetylcholine-binding protein	protein	198	9% helix, 47% strand	P58154
J	Acetylcholine-binding protein	protein	204	8% helix, 47% strand	P58154
K	Acetylcholine-binding protein	protein	203	8% helix, 46% strand	P58154
L	Acetylcholine-binding protein	protein	201	8% helix, 47% strand	P58154
M	Acetylcholine-binding protein	protein	207	10% helix, 48% strand	P58154
N	Acetylcholine-binding protein	protein	203	10% helix, 47% strand	P58154
O	Acetylcholine-binding protein	protein	199	9% helix, 48% strand	P58154
Q	Acetylcholine-binding protein	protein	198	8% helix, 47% strand	P58154
R	Acetylcholine-binding protein	protein	201	8% helix, 47% strand	P58154
S	Acetylcholine-binding protein	protein	198	9% helix, 47% strand	P58154
T	Acetylcholine-binding protein	protein	204	8% helix, 46% strand	P58154

Ligands and binding sites

09P · 1-(5-ethoxypyridin-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
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, G, R
SO4 · Sulfate ion · ion · 10 copies · chains B, C, D, H, I, K, O, L, M, N, P, T, S

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	1051	0.76	0.78	116	09P, SO4
2	652	0.71	0.79	75	09P
3	427	0.68	0.80	50	empty
4	519	0.68	0.78	63	empty
5	411	0.67	0.80	50	empty

Interfaces

25 interfaces between chains.

A–E · 1445 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1388 Å² buried · 18 hydrogen bonds · protein-protein
L–M · 1387 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1382 Å² buried · 20 hydrogen bonds · protein-protein
F–J · 1379 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

3U8K · Crystal structure of the acetylcholine binding protein (AChBP) from Lymnaea stagnalis in… · the same entry in another collection · chain M against M, 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 3U8K · PDBe 3U8K · UniProt P58154

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