MolNFT v1 · #133517 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with Z445856640
5S2K · Non-structural protein 3: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with…”. X-ray diffraction, 1 ligand (VZP), 4 pockets (best druggability 0.66). MolNFT v1 #133517 on…
- PDB
- 5S2K
- 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
- VZP
- Pockets
- 4 · best druggability 0.66
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 | 165 | 41% helix, 19% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 169 | 41% helix, 20% strand | P0DTD1 |
Ligands and binding sites
- VZP · N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.66 | 0.79 | 36 | empty |
| 2 | 157 | 0.53 | 0.79 | 31 | empty |
| 3 | 145 | 0.52 | 0.79 | 24 | empty |
| 4 | 50 | 0.25 | 0.73 | 13 | VZP |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5S2K · PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in… · the same entry in another collection · chain B against B, 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 5S2K · PDBe 5S2K · UniProt P0DTD1
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