MolNFT v1 · #184716 · protein
Human mitochondrial lon protease with substrate in the ATPase domain
7P09 · Lon protease homolog, mitochondrial: “Human mitochondrial lon protease with substrate in the ATPase domain”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #184716 on GenesisL1: 3D…
- PDB
- 7P09
- Type
- protein
- Length
- 3,196 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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 A 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 P36776
- Elsewhere: RCSB PDB 7P09 · PDBe 7P09 · UniProt P36776
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