Research workbench
Crystal structure of the SARS cov-2 papain-like protease in complex with peptide inhibitor VIR250
Analyse Crystal structure of the SARS cov-2 papain-like protease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WUU
- Type
- protein
- Length
- 1,286 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3; VIR250
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- ACE, GVE, ZN, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 318 | 26% helix, 35% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 321 | 24% helix, 35% strand | P0DTD1 |
| C | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 317 | 26% helix, 35% strand | P0DTD1 |
| D | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 318 | 26% helix, 35% strand | P0DTD1 |
| G, H, I, J | VIR250 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, C, G, I, B, D, H, J
- GVE · Methyl 4-aminobutanoate · ligand · 4 copies · chains A, G, B, H, C, I, D, J
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.85 | 0.86 | 110 | GVE |
| 2 | 991 | 0.84 | 0.85 | 107 | GVE |
| 3 | 1032 | 0.84 | 0.85 | 114 | ACE, GVE, MG |
| 4 | 546 | 0.78 | 0.84 | 71 | ACE, GVE |
| 5 | 168 | 0.51 | 0.78 | 27 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1441 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1435 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 726 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 370 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 370 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 8 modified (covalent ligand, nonstandard).
Compared structures
- 6WUU · Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide… · 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 P0DTD1
- Elsewhere: RCSB PDB 6WUU · PDBe 6WUU · UniProt P0DTD1
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