MolNFT v1 · #134068 · protein
Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with Z5198562509 - (R) and (S) isomers
5SRO · Non-structural protein 3: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with…”. X-ray diffraction, 2 ligands (RCR, RD6), 3 pockets (best druggability 0.66). MolNFT v1 #134068 on…
- PDB
- 5SRO
- 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
- RCR, RD6
- Pockets
- 3 · best druggability 0.66
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
- RCR · (8R)-6-(7-bromo-9H-pyrimido[4,5-b]indol-4-yl)-8-fluoro-6-azaspiro[3.4]octane-8-carboxylic acid · ligand · chains A
- RD6 · (8S)-6-(7-bromo-9H-pyrimido[4,5-b]indol-4-yl)-8-fluoro-6-azaspiro[3.4]octane-8-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 | 457 | 0.66 | 0.78 | 35 | empty |
| 2 | 165 | 0.54 | 0.79 | 30 | empty |
| 3 | 136 | 0.52 | 0.80 | 25 | RCR, RD6 |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5SRO · 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 5SRO · PDBe 5SRO · UniProt P0DTD1
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