Research workbench
Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2
Analyse Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VXS
- Type
- protein
- Length
- 334 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
- SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 167 | 41% helix, 20% strand | P0DTD1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.57 | 0.78 | 40 | SO4 |
| 2 | 186 | 0.49 | 0.76 | 27 | SO4 |
| 3 | 168 | 0.45 | 0.75 | 26 | SO4 |
Interfaces
1 interface between chains.
- A–B · 266 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VXS · Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 · 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 6VXS · PDBe 6VXS · UniProt P0DTD1
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