Research workbench
Covalent complex of SARS-cov main protease with N-[(2S)-1-({(2S,3S)-3, 4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-YL]BUTAN-2-YL}AMINO)-4-methyl- 1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Analyse Covalent complex of SARS-cov main protease with N-[(2S)-1-({(2S,3S)-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XHL
- Type
- protein
- Length
- 600 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
- P0C6U8
- Ligands
- V2M
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 301 | 26% helix, 30% strand | P0C6U8 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 26% helix, 29% strand | P0C6U8 |
Ligands and binding sites
- V2M · N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.71 | 0.77 | 63 | empty |
| 2 | 531 | 0.63 | 0.75 | 67 | empty |
| 3 | 179 | 0.51 | 0.78 | 36 | empty |
| 4 | 185 | 0.49 | 0.77 | 25 | V2M |
| 5 | 175 | 0.49 | 0.77 | 23 | V2M |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XHL · Covalent complex of SARS-CoV main protease with… · 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 P0C6U8
- Elsewhere: RCSB PDB 6XHL · PDBe 6XHL · UniProt P0C6U8
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