MolNFT v1 · #175787 · protein
Crystal structure of the SARS-cov-2 main protease complexed with GC376
7D1M · 3C-like proteinase: “Crystal structure of the SARS-cov-2 main protease complexed with GC376”. X-ray diffraction, 1 ligand (K36), 6 pockets (best druggability 0.73). MolNFT v1 #175787 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7D1M
- Type
- protein
- Length
- 609 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- K36
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- K36 · (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.73 | 0.78 | 59 | DMS |
| 2 | 403 | 0.65 | 0.79 | 45 | K36 |
| 3 | 332 | 0.54 | 0.74 | 43 | empty |
| 4 | 215 | 0.53 | 0.77 | 33 | empty |
| 5 | 188 | 0.51 | 0.78 | 24 | K36 |
Interfaces
1 interface between chains.
- A–B · 1246 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7D1M · CRYSTAL STRUCTURE OF THE SARS-CoV-2 MAIN PROTEASE COMPLEXED WITH GC376 · 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 7D1M · PDBe 7D1M · UniProt P0DTD1
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