Research workbench
Crystal structures of the staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors
Analyse Crystal structures of the staphylococcus aureus peptide deformylase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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