MolNFT v1 · #73213 · protein

Structure of ybbd in complex with pugnac

3NVD · Uncharacterized lipoprotein ybbd: “Structure of ybbd in complex with pugnac”. X-ray diffraction, 2 ligands (OAN, NA), 11 pockets (best druggability 0.75). MolNFT v1 #73213 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3NVD
Type: protein
Length: 1,234 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized lipoprotein ybbd
EC: 3.2.1.52
UniProt: P40406
Ligands: OAN, 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 (EC 3.2.1.52)	protein	617	41% helix, 15% strand	P40406

Ligands and binding sites

OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · 4 copies · chains A, B
PG4 · Tetraethylene glycol · additive · chains A

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

Pockets

11 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	872	0.75	0.79	75	empty
2	251	0.59	0.79	31	empty
3	237	0.59	0.80	37	empty
4	226	0.57	0.79	23	empty
5	161	0.56	0.81	30	OAN

Interfaces

1 interface between chains.

A–B · 505 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3NVD · Structure of YBBD in complex with pugnac · 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 3NVD · PDBe 3NVD · UniProt P40406

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