MolNFT v1 · #168700 · protein
Structure of the SARS-cov-2 macrodomain (NSP3) in complex with ADP- ribose
6WOJ · Non-structural protein 3: “Structure of the SARS-cov-2 macrodomain (NSP3) in complex with ADP- ribose”. X-ray diffraction, 1 ligand (APR), 5 pockets (best druggability 0.66). MolNFT v1 #168700 on GenesisL1: 3D structure, binding…
- PDB
- 6WOJ
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- 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
- APR
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 169 | 38% helix, 20% strand | P0DTD1 |
| B, D | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 170 | 38% helix, 20% strand | P0DTD1 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, D, B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.66 | 0.79 | 49 | APR |
| 2 | 408 | 0.65 | 0.79 | 45 | APR |
| 3 | 209 | 0.61 | 0.82 | 32 | APR |
| 4 | 202 | 0.59 | 0.81 | 31 | APR |
| 5 | 202 | 0.47 | 0.74 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–D · 296 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 132 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WOJ · Structure of the SARS-CoV-2 macrodomain (NSP3) in complex with ADP-ribose · 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 6WOJ · PDBe 6WOJ · UniProt P0DTD1
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