MolNFT v1 · #169385 · protein
SARS cov-2 plpro in complex with ubiquitin propargylamide
6XAA · Non-structural protein 3: “SARS cov-2 plpro in complex with ubiquitin propargylamide”. X-ray diffraction, 2 ligands (AYE, ZN), 3 pockets (best druggability 0.67). MolNFT v1 #169385 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XAA
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3; Ubiquitin-propargylamide
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1, J3QS39
- Ligands
- AYE, ZN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 309 | 27% helix, 37% strand | P0DTD1 |
| B | Ubiquitin-propargylamide | protein | 75 | 16% helix, 33% strand | J3QS39 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.67 | 0.80 | 42 | empty |
| 2 | 113 | 0.48 | 0.80 | 26 | empty |
| 3 | 68 | 0.43 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1009 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XAA · SARS CoV-2 PLpro in complex with ubiquitin propargylamide · 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
- Every structure of UniProt J3QS39
- Elsewhere: RCSB PDB 6XAA · PDBe 6XAA · UniProt P0DTD1 · UniProt J3QS39
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