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Crystal structure of lpxc from pseudomonas aeruginosa in complex with ligand PT802
Analyse Crystal structure of lpxc from pseudomonas aeruginosa in complex with ligand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E54
- 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
- HUM, JCG, CA, ZN, CL
- Pockets
- 3 · best druggability 0.76
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
- HUM · (2S)-4-{4-[4-(benzyloxy)-2-fluorophenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl) butanamide · ligand · chains A
- JCG · (2R)-4-{4-[4-(benzyloxy)-2-fluorophenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl) butanamide · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 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 | 76 | 0.76 | 0.98 | 21 | empty |
| 2 | 352 | 0.67 | 0.81 | 41 | HUM, JCG, ZN, CL |
| 3 | 54 | 0.39 | 0.81 | 17 | empty |
Compared structures
- 6E54 · Crystal structure of LpxC from Pseudomonas aeruginosa in complex with ligand PT802 · 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 6E54 · PDBe 6E54 · UniProt P47205
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