Research workbench
Molecular basis for the ATPase-powered substrate translocation by the lon aaa+ protease
Analyse Molecular basis for the ATPase-powered substrate translocation by the lon aaa+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WQH
- Type
- protein
- Length
- 3,234 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease; IG2 substrate
- EC
- 3.4.21.53
- UniProt
- A0A059VAZ3
- Ligands
- 4KZ, AGS, ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, D, E | Lon protease (EC 3.4.21.53) | protein | 537 | 41% helix, 17% strand | A0A059VAZ3 |
| C | Lon protease (EC 3.4.21.53) | protein | 538 | 40% helix, 14% strand | A0A059VAZ3 |
| S | IG2 substrate | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- 4KZ · N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · 6 copies · chains A, B, C, F, D, E
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains F, 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 | 1135 | 0.84 | 0.85 | 137 | ADP |
| 2 | 973 | 0.83 | 0.84 | 107 | ADP |
| 3 | 679 | 0.81 | 0.86 | 64 | AGS |
| 4 | 265 | 0.81 | 0.93 | 31 | empty |
| 5 | 292 | 0.78 | 0.90 | 48 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3612 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 3550 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3425 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2243 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 2034 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 6WQH · Molecular basis for the ATPase-powered substrate translocation by the Lon AAA+ protease · the same entry in another collection · chain B against B, 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 A0A059VAZ3
- Elsewhere: RCSB PDB 6WQH · PDBe 6WQH · UniProt A0A059VAZ3
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