Research workbench
Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41Q mutant
Analyse Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41Q… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PN5
- Type
- protein
- Length
- 181 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Arabidopsis thaliana
- Molecule
- Peptide deformylase 1B, chloroplastic
- EC
- 3.5.1.88
- UniProt
- Q9FUZ2
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase 1B, chloroplastic (EC 3.5.1.88) | protein | 181 | 34% helix, 26% strand | Q9FUZ2 |
Ligands and binding sites
- 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.42 | 0.77 | 21 | empty |
Compared structures
- 3PN5 · Crystal structure of arabidopsis thaliana petide deformylase 1B (ATPDF1B) G41Q 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 A 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 3PN5 · PDBe 3PN5 · UniProt Q9FUZ2
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