Research workbench
Lon protease proteolytic domain complexed with covalent boronic acid inhibitor
Analyse Lon protease proteolytic domain complexed with covalent boronic acid inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1M
- Type
- protein
- Length
- 577 residues
- Chains
- 3
- 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
- UKS
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 196 | 37% helix, 26% strand | P36776 |
| B | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 188 | 35% helix, 27% strand | P36776 |
| C | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 193 | 38% helix, 24% strand | P36776 |
Ligands and binding sites
- UKS · [(1R)-4-phenyl-1-{[N-(pyrazine-2-carbonyl)-D-norvalyl]amino}butyl]boronic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.74 | 0.82 | 59 | empty |
| 2 | 406 | 0.67 | 0.79 | 50 | empty |
| 3 | 73 | 0.58 | 0.88 | 19 | UKS |
| 4 | 101 | 0.56 | 0.85 | 31 | UKS |
| 5 | 65 | 0.52 | 0.86 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 857 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 757 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 558 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6X1M · Lon protease proteolytic domain complexed with covalent boronic acid inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P36776 · AlphaFold monomer V2.0 prediction for lon protease homolog, mitochondrial (P36776) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 6X1M · PDBe 6X1M · UniProt P36776
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