Research workbench
Crystal structure of lpxc from pseudomonas aeruginosa in complex with PT805
Analyse Crystal structure of lpxc from pseudomonas aeruginosa in complex with PT805 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CAX
- 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
- B7UZI4
- Ligands
- EUY, ZN, CL
- Pockets
- 3 · best druggability 0.68
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 | B7UZI4 |
Ligands and binding sites
- EUY · (2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-{2-oxo-4-[4-(2H-1,2,3-triazol-2-yl)phenyl]pyridin-1(2H)-yl}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 · 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 | 173 | 0.68 | 0.87 | 28 | EUY |
| 2 | 355 | 0.67 | 0.81 | 43 | EUY, ZN, CL |
| 3 | 67 | 0.42 | 0.81 | 18 | empty |
Compared structures
- 6CAX · Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PT805 · the same entry in another collection · chain A against A, TM-score 1.00
- B7UZI4 · 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 B7UZI4
- Elsewhere: RCSB PDB 6CAX · PDBe 6CAX · UniProt B7UZI4
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