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Crystal structure of the complex of acetylcholine binding protein and D-tubocurarine

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

PDB: 3PMZ
Type: protein
Length: 2,119 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble acetylcholine receptor
UniProt: Q8WSF8
Ligands: TUB, MG
Pockets: 20 · best druggability 0.77

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Soluble acetylcholine receptor	protein	213	12% helix, 48% strand	Q8WSF8
B	Soluble acetylcholine receptor	protein	211	11% helix, 45% strand	Q8WSF8
C	Soluble acetylcholine receptor	protein	215	13% helix, 49% strand	Q8WSF8
D	Soluble acetylcholine receptor	protein	214	12% helix, 48% strand	Q8WSF8
E	Soluble acetylcholine receptor	protein	211	11% helix, 53% strand	Q8WSF8
F	Soluble acetylcholine receptor	protein	207	10% helix, 49% strand	Q8WSF8
G	Soluble acetylcholine receptor	protein	211	12% helix, 47% strand	Q8WSF8
H	Soluble acetylcholine receptor	protein	212	12% helix, 45% strand	Q8WSF8
I	Soluble acetylcholine receptor	protein	212	12% helix, 48% strand	Q8WSF8
J	Soluble acetylcholine receptor	protein	213	10% helix, 52% strand	Q8WSF8

Ligands and binding sites

TUB · (1beta,1'alpha)-7',12'-dihydroxy-6,6'-dimethoxy-2,2',2'-trimethyltubocuraran-2'-ium · ligand · chains D, E
MG · Magnesium ion · metal · 16 copies · chains A, E, B, C, D, F, G, J, 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	964	0.77	0.79	66	empty
2	1085	0.73	0.77	71	empty
3	1038	0.73	0.76	71	empty
4	1173	0.72	0.75	74	empty
5	911	0.71	0.76	91	empty

Interfaces

19 interfaces between chains.

F–J · 1425 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 1420 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1397 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1396 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 1393 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

3PMZ · Crystal Structure of the Complex of Acetylcholine Binding Protein and d-tubocurarine · 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 3PMZ · PDBe 3PMZ · UniProt Q8WSF8

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