Research workbench
Crystal structure of hcov-NL63 main protease with PF07304814
Analyse Crystal structure of hcov-NL63 main protease with PF07304814 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WQH
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6X5
- Ligands
- 80I
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 24% helix, 29% strand | P0C6X5 |
| B | 3C-like proteinase (EC 3.4.22.-) | protein | 297 | 23% helix, 29% strand | P0C6X5 |
Ligands and binding sites
- 80I · [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl) carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.73 | 0.76 | 84 | empty |
| 2 | 802 | 0.70 | 0.76 | 90 | empty |
| 3 | 193 | 0.47 | 0.75 | 30 | 80I |
| 4 | 188 | 0.47 | 0.75 | 30 | 80I |
| 5 | 63 | 0.28 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 949 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7WQH · Crystal structure of HCoV-NL63 main protease with PF07304814 · 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 P0C6X5
- Elsewhere: RCSB PDB 7WQH · PDBe 7WQH · UniProt P0C6X5
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