MolNFT v1 · #168984 · protein
Crystal structure of the SARS cov-2 papain-like protease in complex with peptide inhibitor VIR251
6WX4 · Non-structural protein 3: “Crystal structure of the SARS cov-2 papain-like protease in complex with peptide inhibitor VIR251”. X-ray diffraction, 3 ligands (73O, GVE, ZN), 1 pocket (best druggability 0.43). MolNFT v1 #168984 on…
- PDB
- 6WX4
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3; VIR251
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- 73O, GVE, ZN
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 320 | 26% helix, 36% strand | P0DTD1 |
| I | VIR251 | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- 73O · (2~{S})-2-azanyl-4-(4-hydroxyphenyl)butanoic acid · ligand · chains D, I
- GVE · Methyl 4-aminobutanoate · ligand · chains D, I
- ZN · Zinc ion · metal · chains D
- ACY · Acetic acid · additive · chains D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.43 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- D–I · 186 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6WX4 · Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide… · the same entry in another collection · chain D against D, 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 P0DTD1
- Elsewhere: RCSB PDB 6WX4 · PDBe 6WX4 · UniProt P0DTD1
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