MolNFT v1 · #136766 · protein

Crystal structure of the receptor-binding domain of botulinum neurotoxin type ha

5V38 · Hcha: “Crystal structure of the receptor-binding domain of botulinum neurotoxin type ha”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #136766 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V38
Type: protein
Length: 834 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hcha
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hcha	protein	418	4% helix, 49% strand	—
B	Hcha	protein	416	4% helix, 49% strand	—

Ligands and binding sites

ACY · Acetic acid · additive · 7 copies · chains A, B

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

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	1123	0.76	0.79	87	empty
2	183	0.63	0.84	34	empty
3	55	0.50	0.86	19	ACY
4	125	0.44	0.77	22	empty
5	88	0.35	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 461 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5V38 · Crystal Structure of The Receptor-binding Domain of Botulinum Neurotoxin Type HA · 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
Elsewhere: RCSB PDB 5V38 · PDBe 5V38

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