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Human mitochondrial lon protease with substrate in the ATPase and protease domains
Analyse Human mitochondrial lon protease with substrate in the ATPase and protease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P0M
- Type
- protein
- Length
- 3,220 residues
- Chains
- 13
- 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 0.84
Structure
electron microscopy · 7 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 534 | 46% helix, 16% 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 | 44% helix, 16% strand | P36776 |
| D | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 531 | 44% helix, 16% strand | P36776 |
| F | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 520 | 45% helix, 16% strand | P36776 |
| G | Unknown peptide from human mitochondrial transcription factor a (tfam) | protein | 11 | 0% helix, 9% strand | — |
| I, J, M, H, L, K | Unknown peptide from human mitochondrial transcription factor a (tfam) | protein | 4 | 0% helix, 50% 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 | 483 | 0.84 | 0.91 | 77 | empty |
| 2 | 677 | 0.80 | 0.85 | 71 | empty |
| 3 | 473 | 0.77 | 0.86 | 67 | empty |
| 4 | 557 | 0.76 | 0.83 | 58 | ATP, MG |
| 5 | 826 | 0.76 | 0.80 | 76 | ADP |
Interfaces
17 interfaces between chains.
- C–D · 3154 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3105 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 3096 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 2381 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1865 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7P0M · Human mitochondrial Lon protease with substrate in the ATPase and protease domains · 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 7P0M · PDBe 7P0M · UniProt P36776
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