Research workbench
Human mitochondrial LONP1 with endogenous substrate
Analyse Human mitochondrial LONP1 with endogenous substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KSM
- Type
- protein
- Length
- 3,149 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease homolog, mitochondrial; Unidentified endogenous substrate
- EC
- 3.4.21.53
- UniProt
- P36776
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 526 | 41% helix, 12% strand | P36776 |
| B | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 520 | 42% helix, 13% strand | P36776 |
| C | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 526 | 42% helix, 14% strand | P36776 |
| D | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 525 | 44% helix, 14% strand | P36776 |
| E | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 524 | 42% helix, 15% strand | P36776 |
| F | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 516 | 43% helix, 16% strand | P36776 |
| G | Unidentified endogenous substrate | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E
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 | 1012 | 0.82 | 0.83 | 119 | ATP, MG |
| 2 | 439 | 0.80 | 0.88 | 76 | empty |
| 3 | 514 | 0.77 | 0.85 | 66 | MG, ATP |
| 4 | 546 | 0.77 | 0.84 | 71 | empty |
| 5 | 592 | 0.76 | 0.83 | 67 | ATP, MG |
Interfaces
13 interfaces between chains.
- C–D · 3228 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 3218 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 3201 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2081 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1872 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KSM · Human mitochondrial LONP1 with endogenous substrate · 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 7KSM · PDBe 7KSM · UniProt P36776
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