MolNFT v1 · #64513 · protein
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target
3G5K · Peptide deformylase, mitochondrial: “Structure and activity of human mitochondrial peptide deformylase, a novel cancer target”. X-ray diffraction, 2 ligands (BB2, CO), 8 pockets (best druggability 0.67). MolNFT v1 #64513 on…
- PDB
- 3G5K
- Type
- protein
- Length
- 732 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide deformylase, mitochondrial
- EC
- 3.5.1.88
- UniProt
- Q9HBH1
- Ligands
- BB2, CO
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptide deformylase, mitochondrial (EC 3.5.1.88) | protein | 183 | 32% helix, 32% strand | Q9HBH1 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.67 | 0.78 | 47 | BB2 |
| 2 | 367 | 0.65 | 0.79 | 32 | BB2 |
| 3 | 334 | 0.63 | 0.79 | 32 | BB2 |
| 4 | 331 | 0.62 | 0.78 | 31 | BB2, CO |
| 5 | 74 | 0.34 | 0.75 | 13 | empty |
Interfaces
2 interfaces between chains.
- C–D · 859 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 853 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3G5K · Structure and activity of human mitochondrial peptide deformylase, a novel cancer target · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HBH1 · AlphaFold monomer V2.0 prediction for peptide deformylase, mitochondrial (Q9HBH1) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9HBH1
- Elsewhere: RCSB PDB 3G5K · PDBe 3G5K · UniProt Q9HBH1
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