Research workbench
Yeast mitochondrial processing peptidase beta-E73Q mutant complexed with malate dehydrogenase signal peptide
Analyse Yeast mitochondrial processing peptidase beta-E73Q mutant complexed with malate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HR9
- Type
- protein
- Length
- 3,592 residues
- Chains
- 12
- 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, 1.1.1.37
- UniProt
- P11914, P10507, P17505
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 452 | 43% helix, 17% strand | P11914 |
| B | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 439 | 45% helix, 20% strand | P10507 |
| C | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 448 | 44% helix, 17% strand | P11914 |
| D | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 441 | 45% helix, 20% strand | P10507 |
| E | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 446 | 44% helix, 17% strand | P11914 |
| F | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 443 | 44% helix, 20% strand | P10507 |
| G | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 451 | 43% helix, 17% strand | P11914 |
| H | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 440 | 45% helix, 20% strand | P10507 |
| O, P, Q, R | Malate dehydrogenase (EC 1.1.1.37) | protein | 8 | 0% helix, 25% strand | P17505 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, O, D, P, F, Q, H, R
- 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 | 1177 | 0.84 | 0.85 | 118 | EPE |
| 2 | 670 | 0.80 | 0.84 | 38 | empty |
| 3 | 810 | 0.75 | 0.80 | 82 | empty |
| 4 | 1037 | 0.73 | 0.77 | 99 | empty |
| 5 | 420 | 0.73 | 0.83 | 53 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1717 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1671 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1638 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1272 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1HR9 · Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate… · the same entry in another collection · chain R against R, 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
- Every structure of UniProt P17505
- Elsewhere: RCSB PDB 1HR9 · PDBe 1HR9 · UniProt P11914 · UniProt P10507 · UniProt P17505
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