MolNFT v1 · #135578 · protein
Pseudomonas aeruginosa lpxc in complex with chir-090
5U39 · Udp-3-O-acyl-N-acetylglucosamine deacetylase: “Pseudomonas aeruginosa lpxc in complex with chir-090”. X-ray diffraction, 2 ligands (C90, ZN), 2 pockets (best druggability 0.69). MolNFT v1 #135578 on GenesisL1: 3D structure, binding…
- PDB
- 5U39
- Type
- protein
- Length
- 287 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
- C90, ZN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 287 | 24% helix, 34% strand | P47205 |
Ligands and binding sites
- C90 · N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide · ligand · chains A
- ZN · Zinc ion · metal · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.69 | 0.80 | 42 | C90 |
| 2 | 183 | 0.49 | 0.76 | 26 | empty |
Compared structures
- 5U39 · Pseudomonas aeruginosa LpxC in complex with CHIR-090 · 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 5U39 · PDBe 5U39 · UniProt P47205
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