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Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose
Analyse Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W02
- Type
- protein
- Length
- 332 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.121, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- APR
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.5 · 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 | 165 | 39% helix, 19% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 167 | 38% helix, 19% strand | P0DTD1 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.63 | 0.81 | 33 | APR |
| 2 | 197 | 0.59 | 0.81 | 31 | APR |
Interfaces
1 interface between chains.
- A–B · 316 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6W02 · Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in the complex with… · 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 6W02 · PDBe 6W02 · UniProt P0DTD1
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