MolNFT v1 · #80791 · protein
Crystal structures of the staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors
3U7M: “Crystal structures of the staphylococcus aureus peptide deformylase in complex with two classes of new…”. X-ray diffraction, 2 ligands (FHF, ZN), 2 pockets (best druggability 0.56). MolNFT v1 #80791 on GenesisL1: 3D structure…
- PDB
- 3U7M
- Type
- protein
- Length
- 185 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q5HGZ3
- Ligands
- FHF, ZN
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 185 | 28% helix, 24% strand | Q5HGZ3 |
Ligands and binding sites
- FHF · N-((2R,4S)-2-butyl-4-(3-(2-fluorophenyl)ureido)-5-methyl-3-oxohexyl)-N-hydroxyformamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.56 | 0.83 | 21 | FHF |
| 2 | 53 | 0.24 | 0.72 | 15 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3U7M · Crystal structures of the Staphylococcus aureus peptide deformylase in complex with two… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HGZ3 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q5HGZ3) · 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 Q5HGZ3
- Elsewhere: RCSB PDB 3U7M · PDBe 3U7M · UniProt Q5HGZ3
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