MolNFT v1 · #123278 · protein
Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT018
5JF3 · Peptide deformylase: “Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor AT018”. X-ray diffraction, 2 ligands (SF5, ZN), 1 pocket (best druggability 0.52). MolNFT v1 #123278 on GenesisL1: 3D…
- PDB
- 5JF3
- Type
- protein
- Length
- 203 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase
- EC
- 3.5.1.88
- UniProt
- Q8E378
- Ligands
- SF5, ZN
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 203 | 30% helix, 24% strand | Q8E378 |
Ligands and binding sites
- SF5 · methyl 4-({5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl}methyl)benzoate · ligand · chains A
- ZN · Zinc ion · metal · 9 copies · chains A
- ACT · Acetate ion · additive · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.52 | 0.82 | 19 | SF5 |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5JF3 · Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8E378 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q8E378) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8E378
- Elsewhere: RCSB PDB 5JF3 · PDBe 5JF3 · UniProt Q8E378
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