Research workbench
Yeast mitochondrial processing peptidase beta-E73Q mutant
Analyse Yeast mitochondrial processing peptidase beta-E73Q mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HR7
- Type
- protein
- Length
- 3,559 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial processing peptidase alpha subunit; Mitochondrial processing peptidase beta…
- EC
- 3.4.24.64
- UniProt
- P11914, P10507
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 457 | 44% helix, 17% strand | P11914 |
| B | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 439 | 46% helix, 20% strand | P10507 |
| C | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 444 | 45% helix, 17% strand | P11914 |
| D | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 441 | 46% helix, 20% strand | P10507 |
| E | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 448 | 45% helix, 17% strand | P11914 |
| F, H | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 440 | 46% helix, 20% strand | P10507 |
| G | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 450 | 44% helix, 17% strand | P11914 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.85 | 0.85 | 117 | empty |
| 2 | 645 | 0.79 | 0.84 | 39 | empty |
| 3 | 1018 | 0.72 | 0.76 | 126 | empty |
| 4 | 968 | 0.72 | 0.76 | 125 | empty |
| 5 | 588 | 0.71 | 0.80 | 59 | empty |
Interfaces
8 interfaces between chains.
- G–H · 1706 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1693 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1589 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1537 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1296 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1HR7 · Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant · the same entry in another collection · chain H against H, TM-score 1.00
- P11914 · AlphaFold monomer V2.0 prediction for mitochondrial-processing peptidase subunit alpha… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P10507 · AlphaFold monomer V2.0 prediction for mitochondrial-processing peptidase subunit beta… · a predicted model of the same protein · chain D 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 P11914
- Every structure of UniProt P10507
- Elsewhere: RCSB PDB 1HR7 · PDBe 1HR7 · UniProt P11914 · UniProt P10507
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