MolNFT v1 · #125203 · protein

Crystal structure of BONT/A receptor binding domain in complex with vhh C2

5L21 · Botulinum neurotoxin type a: “Crystal structure of BONT/A receptor binding domain in complex with vhh C2”. X-ray diffraction, 6 pockets (best druggability 0.82). MolNFT v1 #125203 on GenesisL1: 3D structure, binding sites and…

PDB: 5L21
Type: protein
Length: 544 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Botulinum neurotoxin type a; Vhh-C2
EC: 3.4.24.69
UniProt: A5HZZ9
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Botulinum neurotoxin type a (EC 3.4.24.69)	protein	425	8% helix, 45% strand	A5HZZ9
B	Vhh-C2	protein	119	10% helix, 48% strand	—

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	713	0.82	0.86	87	empty
2	62	0.67	0.95	22	empty
3	73	0.50	0.84	20	empty
4	206	0.48	0.75	25	empty
5	76	0.37	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 1249 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5L21 · Crystal structure of BoNT/A receptor binding domain in complex with VHH C2 · 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 A5HZZ9
Elsewhere: RCSB PDB 5L21 · PDBe 5L21 · UniProt A5HZZ9

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