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The crystal structure of main protease from mouse hepatitis virus A59 in complex with an inhibitor
Analyse The crystal structure of main protease from mouse hepatitis virus A59 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JIJ
- Type
- protein
- Length
- 901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative polyprotein 1AB; 02J-ala-val-leu-pje-010
- UniProt
- Q66WN6
- Ligands
- 02J, PJE, 010
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Replicative polyprotein 1AB | protein | 297 | 23% helix, 30% strand | Q66WN6 |
| C | Replicative polyprotein 1AB | protein | 298 | 22% helix, 28% strand | Q66WN6 |
| D, E, F | 02J-ala-val-leu-pje-010 | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 02J · 5-methyl-1,2-oxazole-3-carboxylic acid · ligand · 3 copies · chains B, D, C, E, A, F
- PJE · (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid · ligand · 3 copies · chains B, D, C, E, A, F
- 010 · phenylmethanol · ligand · 3 copies · chains B, D, C, E, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.75 | 0.78 | 84 | empty |
| 2 | 1135 | 0.71 | 0.75 | 120 | PJE, 010 |
| 3 | 705 | 0.69 | 0.77 | 59 | empty |
| 4 | 415 | 0.63 | 0.78 | 58 | empty |
| 5 | 125 | 0.45 | 0.77 | 24 | PJE, 010 |
Interfaces
6 interfaces between chains.
- B–A · 1410 Ų buried · 26 hydrogen bonds · protein-protein
- C–A · 540 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 321 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 319 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 313 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent (covalent ligand).
Compared structures
- 6JIJ · The Crystal Structure of Main Protease from Mouse Hepatitis Virus A59 in Complex with an… · 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 Q66WN6
- Elsewhere: RCSB PDB 6JIJ · PDBe 6JIJ · UniProt Q66WN6
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