Research workbench
SARS-cov-2 main protease (mpro) C145A in complex with cleavage site NSP5/6 (P6-P1)
Analyse SARS-cov-2 main protease (mpro) C145A in complex with cleavage site NSP5/6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MB5
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Ser-gly-val-thr-phe-gln
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 28% strand | P0DTD1 |
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 27% helix, 30% strand | P0DTD1 |
| D, C | Ser-gly-val-thr-phe-gln | protein | 6 | 0% helix, 33% strand | P0DTD1 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.78 | 0.80 | 83 | empty |
| 2 | 346 | 0.55 | 0.74 | 58 | empty |
| 3 | 128 | 0.45 | 0.77 | 30 | empty |
| 4 | 158 | 0.43 | 0.74 | 30 | empty |
| 5 | 76 | 0.33 | 0.75 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1466 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 560 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7MB5 · SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp5/6 (P6-P1) · 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 7MB5 · PDBe 7MB5 · UniProt P0DTD1
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