Research workbench
Human mitochondrial LONP1 in complex with bortezomib
Analyse Human mitochondrial LONP1 in complex with bortezomib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KRZ
- Type
- protein
- Length
- 3,139 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease homolog, mitochondrial; Endogenous co-purified substrate
- EC
- 3.4.21.53
- UniProt
- P36776
- Ligands
- BO2, ATP, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 525 | 40% helix, 15% strand | P36776 |
| B | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 526 | 41% helix, 15% strand | P36776 |
| C | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 527 | 41% helix, 15% strand | P36776 |
| D | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 520 | 42% helix, 16% strand | P36776 |
| E | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 517 | 39% helix, 15% strand | P36776 |
| F | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 512 | 40% helix, 15% strand | P36776 |
| G | Endogenous co-purified substrate | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- BO2 · N-[(1R)-1-(dihydroxyboryl)-3-methylbutyl]-N-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · 6 copies · chains A, B, C, D, E, F
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 955 | 0.85 | 0.86 | 126 | ATP, MG |
| 2 | 975 | 0.80 | 0.81 | 90 | ATP, MG |
| 3 | 495 | 0.79 | 0.87 | 79 | empty |
| 4 | 574 | 0.79 | 0.85 | 62 | empty |
| 5 | 590 | 0.78 | 0.84 | 65 | ATP, MG |
Interfaces
12 interfaces between chains.
- B–C · 3176 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3086 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3035 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2154 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2138 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
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 7KRZ · PDBe 7KRZ · UniProt P36776
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