MolNFT v1 · #178350 · protein
A complete three-dimensional structure of the lon protease translocating a protein substrate (conformation 2)
7FD5: “A complete three-dimensional structure of the lon protease translocating a protein substrate (conformation 2)”. Electron microscopy, 3 ligands (4KZ, ADP, AGS), 20 pockets (best druggability 0.86). MolNFT v1 #178350 on GenesisL1: 3D…
- PDB
- 7FD5
- Type
- protein
- Length
- 4,696 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease; Alpha-S1-casein
- EC
- 3.4.21.53
- UniProt
- A0A059VAZ3
- Ligands
- 4KZ, ADP, AGS
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, B, D, C, E, A | Lon protease (EC 3.4.21.53) | protein | 779 | 38% helix, 14% strand | A0A059VAZ3 |
| S | Alpha-S1-casein | protein | 22 | 0% helix, 14% strand | — |
Ligands and binding sites
- 4KZ · N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · 6 copies · chains F, B, D, C, E, A
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains F, D, E
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains B, C, D, A
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 | 1119 | 0.86 | 0.87 | 113 | AGS |
| 2 | 1159 | 0.85 | 0.86 | 116 | empty |
| 3 | 1074 | 0.85 | 0.86 | 130 | empty |
| 4 | 808 | 0.84 | 0.87 | 74 | AGS |
| 5 | 745 | 0.84 | 0.88 | 66 | AGS |
Interfaces
19 interfaces between chains.
- D–C · 3641 Ų buried · 34 hydrogen bonds · protein-protein
- B–A · 3625 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 3238 Ų buried · 24 hydrogen bonds · protein-protein
- F–E · 2905 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2301 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7FD5 · A complete three-dimensional structure of the Lon protease translocating a protein… · the same entry in another collection · chain F against F, 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 7FD5 · PDBe 7FD5 · UniProt A0A059VAZ3
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