Research workbench
Lon protease proteolytic domain complexed with bortezomib
Analyse Lon protease proteolytic domain complexed with bortezomib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X27
- Type
- protein
- Length
- 2,249 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease homolog, mitochondrial
- EC
- 3.4.21.53
- UniProt
- P36776
- Ligands
- BO2
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 8 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 186 | 37% helix, 28% strand | P36776 |
| B, F | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 185 | 36% helix, 28% strand | P36776 |
| C | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 194 | 38% helix, 27% strand | P36776 |
| D, E | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 185 | 36% helix, 28% strand | P36776 |
| G | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 184 | 37% helix, 28% strand | P36776 |
| H | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 193 | 38% helix, 27% strand | P36776 |
| I, J, K | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 186 | 36% helix, 28% strand | P36776 |
| L | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 194 | 37% helix, 27% strand | P36776 |
Ligands and binding sites
- BO2 · N-[(1R)-1-(dihydroxyboryl)-3-methylbutyl]-N-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 6 copies · chains A, G, B, K, C, L, F, J, E, H, D, I
- GOL · Glycerol · additive · 2 copies · chains G, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.60 | 0.76 | 75 | BO2 |
| 2 | 328 | 0.57 | 0.76 | 36 | empty |
| 3 | 272 | 0.56 | 0.77 | 42 | empty |
| 4 | 266 | 0.56 | 0.77 | 40 | empty |
| 5 | 253 | 0.55 | 0.77 | 47 | BO2 |
Interfaces
18 interfaces between chains.
- G–J · 758 Ų buried · 13 hydrogen bonds · protein-protein
- D–K · 751 Ų buried · 14 hydrogen bonds · protein-protein
- H–K · 749 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 746 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 744 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 6X27 · Lon protease proteolytic domain complexed with bortezomib · the same entry in another collection · chain L against L, 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 6X27 · PDBe 6X27 · UniProt P36776
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