Research workbench
Structure of Peptide Deformylase from Staphylococcus aureus at 1.45 A
Analyse Structure of Peptide Deformylase from Staphylococcus aureus at 1.45 A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LM4
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Staphylococcus aureus
- Molecule
- peptide deformylase PDF1
- EC
- 3.5.1.88
- UniProt
- P68826
- Ligands
- FE
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.45 · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | peptide deformylase PDF1 (EC 3.5.1.88) | protein | 190 | 28% helix, 25% strand | P68826 |
| B | peptide deformylase PDF1 (EC 3.5.1.88) | protein | 184 | 28% helix, 26% strand | P68826 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.71 | 0.81 | 39 | empty |
| 2 | 132 | 0.49 | 0.79 | 25 | GOL |
| 3 | 58 | 0.34 | 0.77 | 15 | empty |
| 4 | 69 | 0.31 | 0.74 | 14 | empty |
| 5 | 52 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 747 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1LM4 · Structure of peptide deformylase from staphylococcus aureus at 1.45 a · the same entry in another collection · chain A against A, TM-score 1.00
- P68826 · AlphaFold monomer V2.0 prediction for peptide deformylase (P68826) · a predicted model of the same protein · chain B 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 P68826
- Elsewhere: RCSB PDB 1LM4 · PDBe 1LM4 · UniProt P68826
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