MolNFT v1 · #95980 · protein

Structure of lpxi D225A mutant

4J6E · Udp-2,3-diacylglucosamine pyrophosphatase lpxi: “Structure of lpxi D225A mutant”. X-ray diffraction, 1 ligand (UDG), 2 pockets (best druggability 0.80). MolNFT v1 #95980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4J6E
Type: protein
Length: 273 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: UDG
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-2,3-diacylglucosamine pyrophosphatase lpxi (EC 3.6.1.54)	protein	273	41% helix, 18% strand	B8GWR0

Ligands and binding sites

UDG · (2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[(3R)-3-hydroxytetradecanoyl]amino}tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate · ligand · chains A

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

Pockets

2 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	781	0.80	0.83	75	UDG
2	111	0.47	0.79	19	empty

Compared structures

4J6E · Structure of LPXI D225A Mutant · the same entry in another collection · 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 B8GWR0
Elsewhere: RCSB PDB 4J6E · PDBe 4J6E · UniProt B8GWR0

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