MolNFT v1 · #95872 · protein
Pseudomonas aeruginosa lpxc in complex with a hydroxamate inhibitor
4J3D · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Pseudomonas aeruginosa lpxc in complex with a hydroxamate inhibitor”. X-ray diffraction, 2 ligands (1JS, ZN), 6 pockets (best druggability 0.69). MolNFT v1 #95872 on…
- PDB
- 4J3D
- Type
- protein
- Length
- 573 residues
- Chains
- 2
- 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
- 1JS, ZN
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 287 | 24% helix, 35% strand | P47205 |
| B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 286 | 24% helix, 36% strand | P47205 |
Ligands and binding sites
- 1JS · N~1~-hydroxy-N~5~-(3-hydroxypropyl)-N~2~-[4-(phenylethynyl)benzoyl]-L-glutamamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.69 | 0.79 | 66 | ZN, 1JS |
| 2 | 138 | 0.69 | 0.89 | 26 | empty |
| 3 | 547 | 0.66 | 0.77 | 65 | ZN, 1JS |
| 4 | 165 | 0.57 | 0.81 | 24 | empty |
| 5 | 100 | 0.55 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 480 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4J3D · Pseudomonas aeruginosa LpxC in complex with a hydroxamate inhibitor · 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 4J3D · PDBe 4J3D · UniProt P47205
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