MolNFT v1 · #106125 · protein
Crystal structure of human presequence protease in complex with inhibitor mitoblock-60
4RPU · Presequence protease, mitochondrial: “Crystal structure of human presequence protease in complex with inhibitor mitoblock-60”. X-ray diffraction, 3 ligands (3UE, ZN, CA), 20 pockets (best druggability 0.85). MolNFT v1 #106125 on…
- PDB
- 4RPU
- Type
- protein
- Length
- 1,967 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Presequence protease, mitochondrial
- EC
- 3.4.24.-
- UniProt
- Q5JRX3
- Ligands
- 3UE, ZN, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Presequence protease, mitochondrial (EC 3.4.24.-) | protein | 988 | 46% helix, 21% strand | Q5JRX3 |
| B | Presequence protease, mitochondrial (EC 3.4.24.-) | protein | 979 | 47% helix, 21% strand | Q5JRX3 |
Ligands and binding sites
- 3UE · [4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone · ligand · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · 18 copies · chains A, B
- ACT · Acetate ion · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.85 | 0.89 | 89 | empty |
| 2 | 101 | 0.76 | 0.97 | 26 | empty |
| 3 | 190 | 0.73 | 0.89 | 34 | empty |
| 4 | 821 | 0.72 | 0.77 | 75 | ACT |
| 5 | 528 | 0.69 | 0.78 | 37 | 3UE, GOL |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 76 modified (methylation, artifact).
Compared structures
- 4RPU · Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JRX3 · AlphaFold monomer V2.0 prediction for presequence protease, mitochondrial (Q5JRX3) · 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 Q5JRX3
- Elsewhere: RCSB PDB 4RPU · PDBe 4RPU · UniProt Q5JRX3
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