Research workbench
SARS-cov-2 main protease (mpro) C145A in complex with cleavage site NSP4/5 (P6-P1)
Analyse SARS-cov-2 main protease (mpro) C145A in complex with cleavage site NSP4/5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MB4
- Type
- protein
- Length
- 1,244 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Thr-ser-ala-val-leu-gln
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C, B | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 25% helix, 29% strand | P0DTD1 |
| E, H, G, F | Thr-ser-ala-val-leu-gln | protein | 6 | 0% helix, 50% strand | P0DTD1 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.79 | 0.82 | 93 | empty |
| 2 | 969 | 0.77 | 0.79 | 79 | empty |
| 3 | 1026 | 0.77 | 0.79 | 88 | empty |
| 4 | 295 | 0.53 | 0.75 | 45 | empty |
| 5 | 289 | 0.52 | 0.74 | 41 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1581 Ų buried · 38 hydrogen bonds · protein-protein
- D–C · 1578 Ų buried · 38 hydrogen bonds · protein-protein
- B–F · 554 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 550 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 550 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7MB4 · SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp4/5 (P6-P1) · 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 7MB4 · PDBe 7MB4 · UniProt P0DTD1
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