Research workbench
Yeast mitochondrial processing peptidase
Analyse Yeast mitochondrial processing peptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HR6
- Type
- protein
- Length
- 3,587 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 0.84
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | 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 | 453 | 44% helix, 17% strand | P11914 |
| D, F | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 443 | 45% helix, 20% strand | P10507 |
| E | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 455 | 44% helix, 17% strand | P11914 |
| H | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 440 | 45% helix, 20% strand | P10507 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, D, F, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, E, G
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 | 1174 | 0.84 | 0.85 | 122 | EPE |
| 2 | 645 | 0.80 | 0.85 | 37 | empty |
| 3 | 1033 | 0.72 | 0.75 | 131 | empty |
| 4 | 179 | 0.70 | 0.88 | 39 | empty |
| 5 | 874 | 0.70 | 0.75 | 116 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1800 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1765 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1729 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1690 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1281 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1HR6 · Yeast Mitochondrial Processing Peptidase · the same entry in another collection · chain H against H, 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
- 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
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 1HR6 · PDBe 1HR6 · UniProt P11914 · UniProt P10507
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