Research workbench
SARS-cov-2 main protease in complex with NSP8/9 substrate peptide
Analyse SARS-cov-2 main protease in complex with NSP8/9 substrate peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MGR
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Ala-val-lys-leu-gln-asn-asn-glu
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 29% strand | P0DTD1 |
| B | Ala-val-lys-leu-gln-asn-asn-glu | protein | 8 | 0% helix, 38% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.33 | 0.75 | 15 | empty |
| 2 | 51 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7MGR · SARS-CoV-2 main protease in complex with nsp8/9 substrate peptide · 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 7MGR · PDBe 7MGR · UniProt P0DTD1
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