MolNFT v1 · #68617 · protein
Crystal structure of lon protease from thermococcus onnurineus NA1
3K1J · ATP-dependent protease lon: “Crystal structure of lon protease from thermococcus onnurineus NA1”. X-ray diffraction, 1 ligand (ADP), 12 pockets (best druggability 0.79). MolNFT v1 #68617 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3K1J
- Type
- protein
- Length
- 1,127 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent protease lon
- UniProt
- B6YU74
- Ligands
- ADP
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent protease lon | protein | 566 | 43% helix, 20% strand | B6YU74 |
| B | ATP-dependent protease lon | protein | 561 | 43% helix, 20% strand | B6YU74 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.79 | 0.81 | 99 | ADP |
| 2 | 1143 | 0.77 | 0.79 | 126 | PE8 |
| 3 | 394 | 0.67 | 0.80 | 54 | empty |
| 4 | 171 | 0.54 | 0.80 | 26 | ADP |
| 5 | 142 | 0.48 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3119 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3K1J · Crystal structure of Lon protease from Thermococcus onnurineus NA1 · 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 B6YU74
- Elsewhere: RCSB PDB 3K1J · PDBe 3K1J · UniProt B6YU74
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