Research workbench
Crystal structure of ebselen covalently bound to the main protease (3CLPRO/MPRO) of SARS-cov-2.
Analyse Crystal structure of ebselen covalently bound to the main protease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BFB
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Main protease
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
- UniProt
- P0DTD1
- Ligands
- 9JT, NA
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Main protease (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 301 | 24% helix, 30% strand | P0DTD1 |
| B | Main protease (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-) | protein | 305 | 27% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- 9JT · ~{N}-phenyl-2-selanyl-benzamide · ligand · 5 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.76 | 0.79 | 79 | EDO |
| 2 | 412 | 0.58 | 0.75 | 68 | EDO |
| 3 | 213 | 0.51 | 0.77 | 25 | 9JT |
| 4 | 186 | 0.49 | 0.76 | 28 | empty |
| 5 | 157 | 0.42 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1456 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7BFB · Crystal structure of ebselen covalently bound to the main protease (3CLpro/Mpro) of… · 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 7BFB · PDBe 7BFB · UniProt P0DTD1
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