MolNFT v1 · #183100 · protein
Structure of the hemiacetal complex between the SARS-cov-2 main protease and leupeptin
7NEV · 3C-like proteinase: “Structure of the hemiacetal complex between the SARS-cov-2 main protease and leupeptin”. X-ray diffraction, 2 ligands (ACE, CL), 1 pocket (best druggability 0.48). MolNFT v1 #183100 on GenesisL1: 3D structure…
- PDB
- 7NEV
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Leupeptin
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- ACE, CL
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 26% helix, 28% strand | P0DTD1 |
| B | Leupeptin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- CL · Chloride ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.48 | 0.81 | 20 | DMS |
Interfaces
1 interface between chains.
- A–B · 394 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 7NEV · Structure of the hemiacetal complex between the SARS-CoV-2 Main Protease and Leupeptin · 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 7NEV · PDBe 7NEV · UniProt P0DTD1
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