MolNFT v1 · #153567 · protein
The crystal structure of main protease from mouse hepatitis virus A59 in complex with an inhibitor
6JIJ · Replicative polyprotein 1AB: “The crystal structure of main protease from mouse hepatitis virus A59 in complex with an inhibitor”. X-ray diffraction, 3 ligands (02J, PJE, 010), 6 pockets (best druggability 0.75). MolNFT v1 #153567…
- 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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