Research workbench
Crystal structure of arabidopsis thaliana petide deformylase 1B (ATPDF1B) in complex with inhibitor 21
Analyse Crystal structure of arabidopsis thaliana petide deformylase 1B (ATPDF1B) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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