MolNFT v1 · #179557 · protein
Crystal structure of P. aeruginosa lpxc with N-hydroxyformamide inhibitor 19
7K99 · Udp-3-O-acyl-N-acetylglucosamine deacetylase: “Crystal structure of P. aeruginosa lpxc with N-hydroxyformamide inhibitor 19”. X-ray diffraction, 3 ligands (W4M, ZN, SO4), 6 pockets (best druggability 0.76). MolNFT v1 #179557 on…
- PDB
- 7K99
- Type
- protein
- Length
- 592 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
- W4M, ZN, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 299 | 24% helix, 37% strand | P47205 |
| C | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 293 | 24% helix, 34% strand | P47205 |
Ligands and binding sites
- W4M · (hydroxy{(1S)-1-(methylsulfanyl)-2-[5-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)-1H-benzotriazol-1-yl]ethyl}amino)methanol · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 8 copies · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, C
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 | 109 | 0.76 | 0.96 | 20 | GOL |
| 2 | 105 | 0.74 | 0.95 | 23 | GOL |
| 3 | 477 | 0.72 | 0.81 | 53 | W4M, ZN |
| 4 | 510 | 0.69 | 0.79 | 51 | W4M, SO4 |
| 5 | 240 | 0.55 | 0.78 | 50 | empty |
Interfaces
1 interface between chains.
- A–C · 887 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7K99 · Crystal Structure of P. aeruginosa LpxC with N-Hydroxyformamide inhibitor 19 · 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 7K99 · PDBe 7K99 · UniProt P47205
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