MolNFT v1 · #176355 · protein
Crystal structure of zinc bound SARS-cov-2 main protease
7DK1 · 3C-like proteinase: “Crystal structure of zinc bound SARS-cov-2 main protease”. X-ray diffraction, 3 ligands (GLY, ZN, CL), 6 pockets (best druggability 0.77). MolNFT v1 #176355 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7DK1
- Type
- protein
- Length
- 605 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
- P0DTC1
- Ligands
- GLY, ZN, CL
- Pockets
- 6 · best druggability 0.77
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 | 25% helix, 29% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 25% helix, 29% strand | P0DTC1 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.77 | 0.79 | 85 | empty |
| 2 | 214 | 0.58 | 0.80 | 48 | DMS |
| 3 | 173 | 0.52 | 0.79 | 31 | ZN, GLY |
| 4 | 92 | 0.51 | 0.83 | 24 | empty |
| 5 | 169 | 0.43 | 0.74 | 23 | ZN, DMS, GLY |
Interfaces
1 interface between chains.
- A–B · 1468 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 7DK1 · Crystal structure of Zinc bound SARS-CoV-2 main protease · 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 P0DTC1
- Elsewhere: RCSB PDB 7DK1 · PDBe 7DK1 · UniProt P0DTC1
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