MolNFT v1 · #72657 · protein

Crystal structure of BONT/A lc with jth-nb-7239 peptide

3NF3: “Crystal structure of BONT/A lc with jth-nb-7239 peptide”. X-ray diffraction, 2 ligands (ZN, NI), 5 pockets (best druggability 0.48). MolNFT v1 #72657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NF3
Type: protein
Length: 399 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BONT/A; Jth-NB72-39 inhibitor
UniProt: Q7B8V4
Ligands: ZN, NI
Pockets: 5 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BONT/A	protein	392	31% helix, 20% strand	Q7B8V4
C	Jth-NB72-39 inhibitor	protein	7	57% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A, C
NI · Nickel (II) ion · metal · chains A

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.48	0.86	16	empty
2	82	0.43	0.80	23	empty
3	74	0.36	0.77	21	empty
4	61	0.34	0.77	12	empty
5	55	0.26	0.72	15	empty

Interfaces

1 interface between chains.

A–C · 640 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

3NF3 · Crystal structure of BoNT/A LC with JTH-NB-7239 peptide · the same entry in another collection · chain C against C, 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 Q7B8V4
Elsewhere: RCSB PDB 3NF3 · PDBe 3NF3 · UniProt Q7B8V4

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