Research workbench
SARS-cov-2 macrodomain NSP3B bound to the remdesivir nucleoside gs- 441524
Analyse SARS-cov-2 macrodomain NSP3B bound to the remdesivir nucleoside gs- 441524 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QG7
- Type
- protein
- Length
- 339 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease NSP3
- EC
- 3.4.19.12, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- U08
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 170 | 42% helix, 19% strand | P0DTD1 |
| B | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 169 | 42% helix, 20% strand | P0DTD1 |
Ligands and binding sites
- U08 · (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-F][1, 2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl) oxolane-2-carbonitrile · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.62 | 0.76 | 44 | empty |
| 2 | 199 | 0.56 | 0.79 | 35 | U08 |
| 3 | 178 | 0.55 | 0.79 | 36 | U08, EDO |
Interfaces
1 interface between chains.
- A–B · 241 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7QG7 · SARS-CoV-2 macrodomain Nsp3b bound to the remdesivir nucleoside GS-441524 · 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 7QG7 · PDBe 7QG7 · UniProt P0DTD1
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