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Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant
Analyse Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PN6
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Arabidopsis thaliana
- Molecule
- Peptide deformylase 1B, chloroplastic
- EC
- 3.5.1.88
- UniProt
- Q9FUZ2
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase 1B, chloroplastic (EC 3.5.1.88) | protein | 181 | 35% helix, 24% strand | Q9FUZ2 |
| B | Peptide deformylase 1B, chloroplastic (EC 3.5.1.88) | protein | 183 | 36% helix, 24% strand | Q9FUZ2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.50 | 0.81 | 19 | empty |
| 2 | 108 | 0.43 | 0.77 | 22 | empty |
| 3 | 142 | 0.40 | 0.74 | 21 | ZN |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3PN6 · Crystal structure of arabidopsis thaliana petide deformylase 1B (ATPDF1B) G41M mutant · 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 0.98
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 3PN6 · PDBe 3PN6 · UniProt Q9FUZ2
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