MolNFT v1 · #157096 · protein
Co-crystal structure of P. aeruginosa lpxc-50432 complex
6MOD · Udp-3-O-acyl-N-acetylglucosamine deacetylase: “Co-crystal structure of P. aeruginosa lpxc-50432 complex”. X-ray diffraction, 2 ligands (JWV, MG), 4 pockets (best druggability 0.70). MolNFT v1 #157096 on GenesisL1: 3D structure…
- PDB
- 6MOD
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-acyl-N-acetylglucosamine deacetylase
- EC
- 3.5.1.108
- UniProt
- B7UZI4
- Ligands
- JWV, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 298 | 26% helix, 33% strand | B7UZI4 |
Ligands and binding sites
- JWV · N-[(1S)-2-(hydroxyamino)-1-(3-methoxy-1,1-dioxo-1lambda~6~-thietan-3-yl)-2-oxoethyl]-4-(6-hydroxyhexa-1,3-diyn-1-yl)benzamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.70 | 0.82 | 46 | JWV, GOL |
| 2 | 125 | 0.69 | 0.90 | 27 | GOL |
| 3 | 107 | 0.48 | 0.80 | 26 | empty |
| 4 | 50 | 0.36 | 0.80 | 14 | empty |
Compared structures
- 6MOD · Co-Crystal structure of P. aeruginosa LpxC-50432 complex · the same entry in another collection · chain A against A, TM-score 1.00
- B7UZI4 · 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 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 B7UZI4
- Elsewhere: RCSB PDB 6MOD · PDBe 6MOD · UniProt B7UZI4
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