MolNFT v1 · #166794 · protein
Lon protease from yersinia pestis
6V11: “Lon protease from yersinia pestis”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.76). MolNFT v1 #166794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V11
- Type
- protein
- Length
- 2,915 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease
- EC
- 3.4.21.53
- UniProt
- A0A3N4AY83
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 6 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease (EC 3.4.21.53) | protein | 491 | 37% helix, 16% strand | A0A3N4AY83 |
| B | Lon protease (EC 3.4.21.53) | protein | 496 | 39% helix, 15% strand | A0A3N4AY83 |
| C | Lon protease (EC 3.4.21.53) | protein | 503 | 34% helix, 15% strand | A0A3N4AY83 |
| D | Lon protease (EC 3.4.21.53) | protein | 465 | 40% helix, 14% strand | A0A3N4AY83 |
| E | Lon protease (EC 3.4.21.53) | protein | 464 | 38% helix, 15% strand | A0A3N4AY83 |
| F | Lon protease (EC 3.4.21.53) | protein | 496 | 39% helix, 16% strand | A0A3N4AY83 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, E, F
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 | 1018 | 0.76 | 0.78 | 93 | ADP |
| 2 | 701 | 0.75 | 0.81 | 71 | ADP |
| 3 | 646 | 0.75 | 0.81 | 77 | ADP |
| 4 | 90 | 0.72 | 0.95 | 21 | empty |
| 5 | 763 | 0.72 | 0.78 | 73 | ADP |
Interfaces
5 interfaces between chains.
- E–F · 1698 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 1624 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1608 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1562 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1482 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6V11 · Lon Protease from Yersinia pestis · 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 A0A3N4AY83
- Elsewhere: RCSB PDB 6V11 · PDBe 6V11 · UniProt A0A3N4AY83
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