MolNFT v1 · #168149 · protein
Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in complex with AMP
6W6Y · Non-structural protein 3: “Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in complex with AMP”. X-ray diffraction, 1 ligand (AMP), 3 pockets (best druggability 0.57). MolNFT v1 #168149 on GenesisL1: 3D…
- PDB
- 6W6Y
- 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
- AMP
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 168 | 42% helix, 20% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 167 | 40% helix, 20% strand | P0DTD1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.57 | 0.79 | 29 | MES |
| 2 | 199 | 0.56 | 0.79 | 35 | AMP |
| 3 | 142 | 0.41 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 407 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6W6Y · Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP · 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 6W6Y · PDBe 6W6Y · UniProt P0DTD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.