MolNFT v1 · #75333 · protein
Crystal structure of arabidopsis thaliana petide deformylase 1B (ATPDF1B) in complex with inhibitor 21
3PN3 · Peptide deformylase 1B, chloroplastic: “Crystal structure of arabidopsis thaliana petide deformylase 1B (ATPDF1B) in complex with inhibitor 21”. X-ray diffraction, 2 ligands (PN3, ZN), 3 pockets (best druggability 0.50). MolNFT v1…
- PDB
- 3PN3
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase 1B, chloroplastic
- EC
- 3.5.1.88
- UniProt
- Q9FUZ2
- Ligands
- PN3, ZN
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase 1B, chloroplastic (EC 3.5.1.88) | protein | 181 | 35% helix, 24% strand | Q9FUZ2 |
Ligands and binding sites
- PN3 · tert-butyl {(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl}carbamate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.50 | 0.78 | 24 | empty |
| 2 | 134 | 0.50 | 0.79 | 24 | empty |
| 3 | 158 | 0.41 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3PN3 · Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with… · 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 B against A, TM-score 0.97
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 3PN3 · PDBe 3PN3 · UniProt Q9FUZ2
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