MolNFT v1 · #107755 · protein

Engineered ls-achbp with ALPHA4-ALPHA4 binding pocket in complex with NS3920

4UM3 · Acetylcholine binding protein: “Engineered ls-achbp with ALPHA4-ALPHA4 binding pocket in complex with NS3920”. X-ray diffraction, 3 ligands (09R, NAG, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #107755 on GenesisL1: 3D…

PDB: 4UM3
Type: protein
Length: 7,922 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetylcholine binding protein
UniProt: P58154
Ligands: 09R, NAG, SO4
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 27 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetylcholine binding protein	protein	201	8% helix, 46% strand	P58154
B, k	Acetylcholine binding protein	protein	198	9% helix, 48% strand	P58154
C	Acetylcholine binding protein	protein	201	8% helix, 49% strand	P58154
D, m	Acetylcholine binding protein	protein	201	8% helix, 49% strand	P58154
E	Acetylcholine binding protein	protein	195	9% helix, 50% strand	P58154
F, Z	Acetylcholine binding protein	protein	196	9% helix, 47% strand	P58154
G, I, J, l	Acetylcholine binding protein	protein	200	9% helix, 48% strand	P58154
H, K, Y, i	Acetylcholine binding protein	protein	197	9% helix, 47% strand	P58154
L	Acetylcholine binding protein	protein	195	9% helix, 48% strand	P58154
M	Acetylcholine binding protein	protein	198	9% helix, 47% strand	P58154
N, Q, n	Acetylcholine binding protein	protein	196	9% helix, 47% strand	P58154
O	Acetylcholine binding protein	protein	196	9% helix, 49% strand	P58154
P	Acetylcholine binding protein	protein	201	8% helix, 46% strand	P58154
R	Acetylcholine binding protein	protein	198	9% helix, 48% strand	P58154
S	Acetylcholine binding protein	protein	201	8% helix, 47% strand	P58154
T	Acetylcholine binding protein	protein	194	9% helix, 50% strand	P58154
U	Acetylcholine binding protein	protein	197	9% helix, 49% strand	P58154
V	Acetylcholine binding protein	protein	199	9% helix, 49% strand	P58154
W	Acetylcholine binding protein	protein	197	9% helix, 47% strand	P58154
X	Acetylcholine binding protein	protein	202	8% helix, 47% strand	P58154
a	Acetylcholine binding protein	protein	197	9% helix, 47% strand	P58154
b, e	Acetylcholine binding protein	protein	198	9% helix, 49% strand	P58154
c	Acetylcholine binding protein	protein	200	9% helix, 47% strand	P58154
d	Acetylcholine binding protein	protein	198	9% helix, 47% strand	P58154
f	Acetylcholine binding protein	protein	195	9% helix, 48% strand	P58154
g, j	Acetylcholine binding protein	protein	198	9% helix, 48% strand	P58154
h	Acetylcholine binding protein	protein	199	9% helix, 47% strand	P58154

Ligands and binding sites

09R · 1-(6-bromopyridin-3-yl)-1,4-diazepane · ligand · 40 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, F, O, d
SO4 · Sulfate ion · ion · chains U, V

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	546	0.78	0.85	62	empty
2	1026	0.78	0.80	82	empty
3	761	0.78	0.82	73	empty
4	780	0.78	0.82	59	empty
5	93	0.77	0.98	19	09R

Interfaces

78 interfaces between chains.

D–E · 1483 Å² buried · 17 hydrogen bonds · protein-protein
S–T · 1471 Å² buried · 18 hydrogen bonds · protein-protein
V–W · 1467 Å² buried · 19 hydrogen bonds · protein-protein
F–J · 1457 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1450 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 79 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4UM3 · Engineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3920 · 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 4UM3 · PDBe 4UM3 · UniProt P58154

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