MolNFT v1 · #123281 · protein
Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor 6B (AB47)
5JF6 · Peptide deformylase: “Crystal structure of type 2 pdf from streptococcus agalactiae in complex with inhibitor 6B (AB47)”. X-ray diffraction, 2 ligands (BB4, ZN), 1 pocket (best druggability 0.48). MolNFT v1 #123281 on GenesisL1: 3D…
- PDB
- 5JF6
- 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
- BB4, ZN
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase (EC 3.5.1.88) | protein | 203 | 30% helix, 25% strand | Q8E378 |
Ligands and binding sites
- BB4 · 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide · ligand · chains A
- ZN · Zinc ion · metal · 8 copies · chains A
- ACT · Acetate ion · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.48 | 0.76 | 30 | BB4 |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5JF6 · 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 5JF6 · PDBe 5JF6 · UniProt Q8E378
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