Research workbench
X-ray structure of peptide deformylase from arabidopsis thaliana (ATPDF1A) in complex with met-ala-ser
Analyse X-ray structure of peptide deformylase from arabidopsis thaliana (ATPDF1A) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZY1
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase, mitochondrial; Tripeptide fragment
- EC
- 3.5.1.88
- UniProt
- Q9FV53
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide deformylase, mitochondrial (EC 3.5.1.88) | protein | 191 | 28% helix, 33% strand | Q9FV53 |
| D, E | Tripeptide fragment | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.54 | 0.80 | 27 | empty |
| 2 | 151 | 0.48 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1090 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 337 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 330 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1ZY1 · X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9FV53 · AlphaFold monomer V2.0 prediction for peptide deformylase 1A, CHLOROPLASTIC/MITOCHONDRIAL… · a predicted model of the same protein · chain B 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 Q9FV53
- Elsewhere: RCSB PDB 1ZY1 · PDBe 1ZY1 · UniProt Q9FV53
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