Research workbench
Human mitochondrial Lon protease with substrate in the ATPase domain
Analyse Human mitochondrial Lon protease with substrate in the ATPase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P09
- Type
- protein
- Length
- 3,196 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Lon protease homolog, mitochondrial; Unknown peptide from human mitochondrial…
- EC
- 3.4.21.53
- UniProt
- P36776
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 2.7 · 6 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 534 | 46% helix, 14% strand | P36776 |
| B | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 536 | 45% helix, 15% strand | P36776 |
| C, E | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 532 | 46% helix, 15% strand | P36776 |
| D | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 531 | 45% helix, 16% strand | P36776 |
| F | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 520 | 44% helix, 15% strand | P36776 |
| G | Unknown peptide from human mitochondrial transcription factor A (TFAM) | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains D, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, F
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 | 1125 | 0.87 | 0.88 | 128 | empty |
| 2 | 893 | 0.81 | 0.84 | 108 | ATP, MG |
| 3 | 1131 | 0.81 | 0.82 | 101 | ADP |
| 4 | 566 | 0.79 | 0.85 | 63 | ATP, MG |
| 5 | 547 | 0.78 | 0.85 | 54 | empty |
Interfaces
13 interfaces between chains.
- A–B · 3282 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3281 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3196 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2415 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 1949 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7P09 · Human mitochondrial lon protease with substrate in the ATPase domain · the same entry in another collection · chain G against G, TM-score 1.00
- P36776 · AlphaFold monomer V2.0 prediction for lon protease homolog, mitochondrial (P36776) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P36776
- Elsewhere: RCSB PDB 7P09 · PDBe 7P09 · UniProt P36776
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