MolNFT v1 · #179558 · protein
Crystal structure of P. aeruginosa lpxc with N-hydroxyformamide inhibitor
7K9A · Udp-3-O-acyl-N-acetylglucosamine deacetylase: “Crystal structure of P. aeruginosa lpxc with N-hydroxyformamide inhibitor”. X-ray diffraction, 4 ligands (W4P, W8P, ZN), 8 pockets (best druggability 0.73). MolNFT v1 #179558 on…
- PDB
- 7K9A
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- 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
- W4P, W8P, ZN, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 299 | 25% helix, 37% strand | P47205 |
Ligands and binding sites
- W4P · N-hydroxy-N-[(1S)-2-{5-[(4-{[2-(hydroxymethyl)-1H-imidazol-1-yl]methyl}phenyl)ethynyl]-1H-benzotriazol-1-yl}-1-(methylsulfanyl)ethyl]formamide · ligand · 2 copies · chains A, C
- W8P · N-hydroxy-N-[(1R)-2-{5-[(4-{[2-(hydroxymethyl)-1H-imidazol-1-yl]methyl}phenyl)ethynyl]-1H-benzotriazol-1-yl}-1-(methylsulfanyl)ethyl]formamide · ligand · chains C
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, C
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.73 | 0.96 | 20 | GOL |
| 2 | 88 | 0.73 | 0.95 | 23 | GOL |
| 3 | 512 | 0.69 | 0.79 | 55 | W4P, DMS |
| 4 | 474 | 0.69 | 0.80 | 48 | W4P, ZN |
| 5 | 176 | 0.51 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- A–C · 905 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7K9A · Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
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 7K9A · PDBe 7K9A · UniProt P47205
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