MolNFT v1 · #59072 · protein

Beta-N-hexosaminidase (ybbd) from bacillus subtilis

3BMX · Uncharacterized lipoprotein ybbd: “Beta-N-hexosaminidase (ybbd) from bacillus subtilis”. X-ray diffraction, 2 ligands (P4G, NA), 11 pockets (best druggability 0.75). MolNFT v1 #59072 on GenesisL1: 3D structure, binding sites and…

PDB: 3BMX
Type: protein
Length: 1,234 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized lipoprotein ybbd
UniProt: P40406
Ligands: P4G, NA
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uncharacterized lipoprotein ybbd	protein	617	41% helix, 15% strand	P40406

Ligands and binding sites

P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 3 copies · chains A, B
NA · Sodium ion · metal · 4 copies · chains A, B
ACT · Acetate ion · additive · 7 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1099	0.75	0.78	82	empty
2	187	0.60	0.83	24	empty
3	230	0.60	0.81	28	empty
4	170	0.58	0.81	24	P4G
5	185	0.55	0.79	24	empty

Interfaces

1 interface between chains.

A–B · 651 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3BMX · Beta-N-hexosaminidase (YbbD) from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
P40406 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase (P40406) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P40406
Elsewhere: RCSB PDB 3BMX · PDBe 3BMX · UniProt P40406

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