Research workbench
Crystal structure of SARS-cov-2 macrodomain in complex with remdesivir metabolite gs-441524
Analyse Crystal structure of SARS-cov-2 macrodomain in complex with remdesivir… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BF6
- Type
- protein
- Length
- 507 residues
- Chains
- 3
- 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
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 169 | 43% helix, 20% strand | P0DTD1 |
| B | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 171 | 41% helix, 20% strand | P0DTD1 |
| C | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 167 | 40% 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 · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.57 | 0.79 | 31 | U08, EDO |
| 2 | 211 | 0.56 | 0.78 | 35 | U08 |
| 3 | 177 | 0.54 | 0.79 | 31 | U08 |
| 4 | 61 | 0.28 | 0.73 | 12 | empty |
| 5 | 58 | 0.26 | 0.72 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 598 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BF6 · Crystal structure of SARS-CoV-2 macrodomain in complex with remdesivir metabolite… · 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 7BF6 · PDBe 7BF6 · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.