MolNFT v1 · #167929 · protein
Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in the complex with ADP ribose
6W02 · Non-structural protein 3: “Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in the complex with ADP ribose”. X-ray diffraction, 1 ligand (APR), 2 pockets (best druggability 0.63). MolNFT v1 #167929 on GenesisL1…
- PDB
- 6W02
- Type
- protein
- Length
- 332 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
- APR
- Pockets
- 2 · best druggability 0.63
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 | 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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