MolNFT v1 · #135217 · protein

Crystal structure of achbp from aplysia californica complex with 2- aminopyrimidine at pH 7.0 spacegroup P212121

5TSF · Soluble acetylcholine receptor: “Crystal structure of achbp from aplysia californica complex with 2- aminopyrimidine at pH 7.0 spacegroup…”. X-ray diffraction, 2 ligands (7KO, NAG), 18 pockets (best druggability 0.71). MolNFT v1…

PDB: 5TSF
Type: protein
Length: 1,063 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble acetylcholine receptor
UniProt: Q8WSF8
Ligands: 7KO, NAG
Pockets: 18 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Soluble acetylcholine receptor	protein	211	10% helix, 49% strand	Q8WSF8
B	Soluble acetylcholine receptor	protein	213	12% helix, 45% strand	Q8WSF8
E	Soluble acetylcholine receptor	protein	217	12% helix, 49% strand	Q8WSF8

Ligands and binding sites

7KO · 6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine · ligand · 5 copies · chains A, E, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	645	0.71	0.78	68	7KO
2	641	0.71	0.78	67	7KO
3	470	0.71	0.81	51	7KO
4	531	0.70	0.79	55	7KO
5	577	0.65	0.76	60	7KO

Interfaces

5 interfaces between chains.

A–B · 1392 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1379 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 1369 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1345 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1339 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5TSF · Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH… · 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 5TSF · PDBe 5TSF · UniProt Q8WSF8

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