MolNFT v1 · #96246 · protein
Crystal structure of a human-like mitochondrial peptide deformylase
4JE6 · Peptide deformylase 1A, CHLOROPLASTIC/MITOCHONDRIAL: “Crystal structure of a human-like mitochondrial peptide deformylase”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #96246 on GenesisL1: 3D…
- PDB
- 4JE6
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase 1A, CHLOROPLASTIC/MITOCHONDRIAL
- EC
- 3.5.1.88
- UniProt
- Q9FV53
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide deformylase 1A, CHLOROPLASTIC/MITOCHONDRIAL (EC 3.5.1.88) | protein | 193 | 30% helix, 32% strand | Q9FV53 |
| B | Peptide deformylase 1A, CHLOROPLASTIC/MITOCHONDRIAL (EC 3.5.1.88) | protein | 189 | 30% helix, 32% strand | Q9FV53 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.68 | 0.82 | 33 | empty |
| 2 | 336 | 0.66 | 0.81 | 28 | empty |
| 3 | 51 | 0.25 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1098 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4JE6 · Crystal structure of a human-like mitochondrial peptide deformylase · 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 1.00
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 4JE6 · PDBe 4JE6 · UniProt Q9FV53
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