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Crystal structure of SARS-cov-2 NSP3 macrodomain in complex with ADP- ribose at pH 10 (P43 crystal form)
Analyse Crystal structure of SARS-cov-2 NSP3 macrodomain in complex with ADP- ribose at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TX1
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- AR6
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 166 | 38% helix, 19% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 169 | 41% helix, 19% strand | P0DTD1 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.64 | 0.78 | 35 | empty |
| 2 | 224 | 0.58 | 0.79 | 31 | AR6 |
| 3 | 150 | 0.52 | 0.79 | 23 | empty |
| 4 | 58 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7TX1 · Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 10 (P43… · 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 7TX1 · PDBe 7TX1 · UniProt P0DTD1
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