MolNFT v1 · #134007 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with REAL250001448407 - (S) isomer
5SPZ · Non-structural protein 3: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with…”. X-ray diffraction, 1 ligand (QJC), 3 pockets (best druggability 0.67). MolNFT v1 #134007 on…
- PDB
- 5SPZ
- Type
- protein
- Length
- 336 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
- QJC
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 167 | 40% helix, 19% strand | P0DTD1 |
| B | Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-) | protein | 169 | 42% helix, 19% strand | P0DTD1 |
Ligands and binding sites
- QJC · (3S)-3-(fluoromethyl)-1-(6-oxo-1,6-dihydropyridazine-4-carbonyl)pyrrolidine-3-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.67 | 0.79 | 37 | empty |
| 2 | 156 | 0.54 | 0.80 | 29 | empty |
| 3 | 136 | 0.51 | 0.79 | 23 | QJC |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5SPZ · 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 5SPZ · PDBe 5SPZ · UniProt P0DTD1
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