MolNFT v1 · #116891 · protein
Crystal structure of the pseudomonas aeruginosa LPXC/LPC-058 complex
5DRR · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Crystal structure of the pseudomonas aeruginosa LPXC/LPC-058 complex”. X-ray diffraction, 3 ligands (5EN, ZN, NO3), 3 pockets (best druggability 0.69). MolNFT v1 #116891…
- PDB
- 5DRR
- Type
- protein
- Length
- 296 residues
- Chains
- 1
- 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
- P47205
- Ligands
- 5EN, ZN, NO3
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 296 | 24% helix, 32% strand | P47205 |
Ligands and binding sites
- 5EN · 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3S)-4,4-difluoro-3-hydroxy-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]benzamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NO3 · Nitrate ion · ion · 17 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.69 | 0.80 | 47 | ZN, 5EN, NO3 |
| 2 | 115 | 0.56 | 0.83 | 22 | NO3 |
| 3 | 53 | 0.36 | 0.80 | 15 | empty |
Compared structures
- 5DRR · Crystal structure of the Pseudomonas aeruginosa LpxC/LPC-058 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P47205 · 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 P47205
- Elsewhere: RCSB PDB 5DRR · PDBe 5DRR · UniProt P47205
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