MolNFT v1 · #169695 · protein
The crystal structure of 3CL mainpro of SARS-cov-2 with oxidized CYS145 (sulfenic acid cysteine).
6XKF · 3C-like proteinase: “The crystal structure of 3CL mainpro of SARS-cov-2 with oxidized CYS145 (sulfenic acid cysteine).”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.76). MolNFT v1 #169695 on GenesisL1: 3D…
- PDB
- 6XKF
- Type
- protein
- Length
- 612 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
- CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 306 | 25% helix, 29% strand | P0DTD1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 925 | 0.76 | 0.79 | 73 | CL, EDO |
| 2 | 325 | 0.53 | 0.74 | 42 | empty |
| 3 | 172 | 0.47 | 0.76 | 30 | empty |
| 4 | 173 | 0.45 | 0.75 | 26 | EDO |
| 5 | 158 | 0.44 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1619 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6XKF · The crystal structure of 3CL MainPro of SARS-CoV-2 with oxidized Cys145 (Sulfenic acid… · 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 6XKF · PDBe 6XKF · UniProt P0DTD1
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