MolNFT v1 · #136325 · protein
Crystal structure of lpxc from pseudomonas aeruginosa in complex with pf-5081090
5UPG · Udp-3-O-acyl-N-acetylglucosamine deacetylase: “Crystal structure of lpxc from pseudomonas aeruginosa in complex with pf-5081090”. X-ray diffraction, 3 ligands (8GJ, ZN, CL), 4 pockets (best druggability 0.69). MolNFT v1 #136325 on…
- PDB
- 5UPG
- Type
- protein
- Length
- 300 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
- P47205
- Ligands
- 8GJ, ZN, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 24% 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 | 300 | 24% helix, 33% strand | P47205 |
Ligands and binding sites
- 8GJ · (2R)-4-[4-(2-fluoro-4-methoxyphenyl)-2-oxopyridin-1(2H)-yl]-N-hydroxy-2-methyl-2-(methylsulfonyl) butanamide · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 6 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 | 173 | 0.69 | 0.87 | 28 | 8GJ |
| 2 | 357 | 0.66 | 0.80 | 39 | 8GJ, ZN |
| 3 | 67 | 0.43 | 0.82 | 18 | empty |
| 4 | 50 | 0.33 | 0.78 | 15 | empty |
Compared structures
- 5UPG · Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PF-5081090 · 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 0.99
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 5UPG · PDBe 5UPG · UniProt P47205
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