MolNFT v1 · #73490 · protein
Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in complex with inhibitor 6B
3O3J: “Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in complex with inhibitor 6B”. X-ray diffraction, 2 ligands (BB4, ZN), 1 pocket (best druggability 0.52). MolNFT v1 #73490 on GenesisL1: 3D structure…
- PDB
- 3O3J
- Type
- protein
- Length
- 180 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase 1B
- EC
- 3.5.1.88
- UniProt
- Q9FUZ2
- Ligands
- BB4, ZN
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase 1B (EC 3.5.1.88) | protein | 180 | 35% helix, 28% strand | Q9FUZ2 |
Ligands and binding sites
- BB4 · 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide · ligand · chains A
- ZN · Zinc ion · metal · 6 copies · 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 | 140 | 0.52 | 0.80 | 24 | ZN, BB4 |
Compared structures
- 3O3J · Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FUZ2 · AlphaFold monomer V2.0 prediction for peptide deformylase 1B, CHLOROPLASTIC/MITOCHONDRIAL… · 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 Q9FUZ2
- Elsewhere: RCSB PDB 3O3J · PDBe 3O3J · UniProt Q9FUZ2
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