MolNFT v1 · #133980 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with Z5010894415 - (S) isomer
5SP8 · Non-structural protein 3: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with…”. X-ray diffraction, 1 ligand (RXI), 3 pockets (best druggability 0.67). MolNFT v1 #133980 on…
- PDB
- 5SP8
- 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
- RXI
- 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
- RXI · (6~{S})-7-[4-(cyclopropylcarbamoylamino) phenyl]carbonyl-3-methyl-6,8-dihydro-5~{H}-[1,2, 4]triazolo[4,3-a]pyrazine-6-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 | 455 | 0.67 | 0.79 | 39 | empty |
| 2 | 159 | 0.52 | 0.79 | 30 | RXI |
| 3 | 139 | 0.51 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 525 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5SP8 · PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in… · 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 5SP8 · PDBe 5SP8 · UniProt P0DTD1
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