MolNFT v1 · #102879 · protein

A.AOLICUS lpxc in complex with native product

4OZE · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “A.AOLICUS lpxc in complex with native product”. X-ray diffraction, 3 ligands (24G, ZN, CL), 3 pockets (best druggability 0.82). MolNFT v1 #102879 on GenesisL1: 3D…

PDB: 4OZE
Type: protein
Length: 533 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
EC: 3.5.1.-
UniProt: O67648
Ligands: 24G, ZN, CL
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-)	protein	266	24% helix, 35% strand	O67648
B	Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-)	protein	267	24% helix, 35% strand	O67648

Ligands and binding sites

24G · uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 7 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1148	0.82	0.83	101	ZN, 24G
2	65	0.39	0.79	18	empty
3	60	0.34	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 385 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4OZE · A.aolicus LpxC in complex with native product · the same entry in another collection · chain A against A, TM-score 1.00
O67648 · AlphaFold monomer V2.0 prediction for udp-3-O-acyl-N- acetylglucosamine deacetylase… · a predicted model of the same protein · 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 O67648
Elsewhere: RCSB PDB 4OZE · PDBe 4OZE · UniProt O67648

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