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Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with Z5459166285 - (R,R) and (S,S) isomers
Analyse Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SSP
- 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
- RTI, RTU
- 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
- RTI · (1S,2S)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-carboxylic acid · ligand · chains A
- RTU · (1R,2R)-4-hydroxy-1-[(1H-indole-5-carbonyl)amino]-2,3-dihydro-1H-indene-2-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 | 0.67 | 0.79 | 37 | empty |
| 2 | 157 | 0.54 | 0.80 | 31 | empty |
| 3 | 137 | 0.51 | 0.79 | 25 | RTI, RTU |
Interfaces
1 interface between chains.
- A–B · 528 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5SSP · 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 5SSP · PDBe 5SSP · UniProt P0DTD1
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