Research workbench
Lon protease from yersinia pestis with Y2853 substrate
Analyse Lon protease from yersinia pestis with Y2853 substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ON2
- Type
- protein
- Length
- 3,130 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent protease la; Bound Y2853 substrate
- EC
- 3.4.21.53
- UniProt
- A0A3N4AY83
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | ATP-dependent protease la (EC 3.4.21.53) | protein | 523 | 38% helix, 18% strand | A0A3N4AY83 |
| B | ATP-dependent protease la (EC 3.4.21.53) | protein | 524 | 41% helix, 17% strand | A0A3N4AY83 |
| D | ATP-dependent protease la (EC 3.4.21.53) | protein | 518 | 41% helix, 17% strand | A0A3N4AY83 |
| F | ATP-dependent protease la (EC 3.4.21.53) | protein | 512 | 39% helix, 17% strand | A0A3N4AY83 |
| G | Bound Y2853 substrate | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, 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 | 795 | 0.86 | 0.89 | 112 | empty |
| 2 | 625 | 0.83 | 0.88 | 82 | ATP, MG |
| 3 | 960 | 0.82 | 0.83 | 105 | ADP |
| 4 | 624 | 0.81 | 0.86 | 67 | ATP, MG |
| 5 | 242 | 0.80 | 0.93 | 31 | empty |
Interfaces
15 interfaces between chains.
- B–C · 3382 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3252 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3237 Ų buried · 46 hydrogen bonds · protein-protein
- D–E · 2747 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 2221 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6ON2 · Lon Protease from Yersinia pestis with Y2853 substrate · 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 6ON2 · PDBe 6ON2 · UniProt A0A3N4AY83
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