Research workbench
Crystal structure of SARS COV2 main protease in complex with inhibitor boceprevir
Analyse Crystal structure of SARS COV2 main protease in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRU
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- 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
- U5G
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 26% 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 | 304 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- U5G · boceprevir (bound form) · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.55 | 0.78 | 41 | DMS |
| 2 | 163 | 0.49 | 0.77 | 21 | U5G |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ZRU · Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir · 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 6ZRU · PDBe 6ZRU · UniProt P0DTD1
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