MolNFT v1 · #104513 · protein

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin a complex

4QD2 · Hemagglutinin component HA33: “Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin a complex”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.79). MolNFT v1 #104513 on GenesisL1: 3D…

PDB: 4QD2
Type: protein
Length: 2,303 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin component HA33; Hemagglutinin component HA17; Hemagglutinin component HA70…
UniProt: A5HZZ6, A5HZZ5, A5HZZ4, P09803
Ligands: CA
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 3% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, I, H	Hemagglutinin component HA33	protein	286	5% helix, 49% strand	A5HZZ6
B, G	Hemagglutinin component HA17	protein	143	6% helix, 49% strand	A5HZZ5
A	Hemagglutinin component HA70	protein	224	2% helix, 55% strand	A5HZZ4
E, J	Cadherin-1	protein	212	2% helix, 44% strand	P09803
F	Hemagglutinin component HA70	protein	225	2% helix, 56% strand	A5HZZ4

Ligands and binding sites

CA · Calcium ion · metal · 6 copies · chains E, J

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	737	0.79	0.83	60	empty
2	735	0.79	0.83	66	empty
3	341	0.65	0.80	42	empty
4	349	0.61	0.78	39	empty
5	260	0.58	0.78	35	empty

Interfaces

17 interfaces between chains.

D–C · 1076 Å² buried · 12 hydrogen bonds · protein-protein
I–H · 995 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 924 Å² buried · 19 hydrogen bonds · protein-protein
G–F · 901 Å² buried · 13 hydrogen bonds · protein-protein
F–J · 892 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4QD2 · Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex · the same entry in another collection · chain J against J, TM-score 1.00
P09803 · AlphaFold monomer V2.0 prediction for cadherin-1 (P09803) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 A5HZZ6
Every structure of UniProt A5HZZ5
Every structure of UniProt A5HZZ4
Every structure of UniProt P09803
Elsewhere: RCSB PDB 4QD2 · PDBe 4QD2 · UniProt A5HZZ6 · UniProt A5HZZ5 · UniProt A5HZZ4 · UniProt P09803

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.