MolNFT v1 · #114173 · protein

Crystal structure of H10N mutant of lpxh

5B4D · Udp-2,3-diacylglucosamine hydrolase: “Crystal structure of H10N mutant of lpxh”. X-ray diffraction, 5 pockets (best druggability 0.78). MolNFT v1 #114173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B4D
Type: protein
Length: 465 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-2,3-diacylglucosamine hydrolase
EC: 3.6.1.54
UniProt: Q9I2V0
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54)	protein	232	37% helix, 28% strand	Q9I2V0
B	Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54)	protein	233	36% helix, 27% strand	Q9I2V0

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1041	0.78	0.80	90	GOL
2	442	0.66	0.78	50	empty
3	376	0.64	0.78	45	empty
4	134	0.41	0.75	25	empty
5	89	0.36	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 506 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5B4D · Crystal structure of H10N mutant of LpxH · the same entry in another collection · chain A against A, TM-score 1.00
Q9I2V0 · AlphaFold monomer V2.0 prediction for udp-2,3-diacylglucosamine hydrolase (Q9I2V0) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9I2V0
Elsewhere: RCSB PDB 5B4D · PDBe 5B4D · UniProt Q9I2V0

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