Research workbench
Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) in complex with inhibitor 6B
Analyse Crystal structure of arabidopsis thaliana peptide 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
- 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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