MolNFT v1 · #92703 · protein

Structure of lpxi

4GGM · Udp-2,3-diacylglucosamine pyrophosphatase lpxi: “Structure of lpxi”. X-ray diffraction, 2 ligands (LP5, MG), 1 pocket (best druggability 0.73). MolNFT v1 #92703 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GGM
Type: protein
Length: 277 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-2,3-diacylglucosamine pyrophosphatase lpxi
EC: 3.6.1.54
UniProt: B8GWR0
Ligands: LP5, MG
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Udp-2,3-diacylglucosamine pyrophosphatase lpxi (EC 3.6.1.54)	protein	277	38% helix, 20% strand	B8GWR0

Ligands and binding sites

LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · chains X
MG · Magnesium ion · metal · chains X

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	241	0.73	0.87	32	LP5

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

4GGM · Structure of LpxI · the same entry in another collection · chain X against X, 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 B8GWR0
Elsewhere: RCSB PDB 4GGM · PDBe 4GGM · UniProt B8GWR0

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