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Processive cleavage of substrate at individual proteolytic active sites of the lon protease complex (conformation 3)
Analyse Processive cleavage of substrate at individual proteolytic active sites of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FIZ
- Type
- protein
- Length
- 4,696 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease; Unknown endogenous substrate
- EC
- 3.4.21.53
- UniProt
- A0A059VAZ3
- Ligands
- AGS, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D, E, F, A | Lon protease (EC 3.4.21.53) | protein | 779 | 38% helix, 15% strand | A0A059VAZ3 |
| S | Unknown endogenous substrate | protein | 22 | 0% helix, 0% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains B, C, D, F, A
- ADP · Adenosine-5'-diphosphate · ligand · chains 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 | 346 | 0.85 | 0.94 | 51 | empty |
| 2 | 670 | 0.85 | 0.89 | 59 | AGS |
| 3 | 985 | 0.83 | 0.84 | 94 | AGS |
| 4 | 637 | 0.83 | 0.88 | 66 | AGS |
| 5 | 234 | 0.79 | 0.92 | 57 | empty |
Interfaces
20 interfaces between chains.
- B–A · 3609 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3531 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 3267 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 2920 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2860 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7FIZ · Processive cleavage of substrate at individual proteolytic active sites of the Lon… · 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 7FIZ · PDBe 7FIZ · UniProt A0A059VAZ3
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