Research workbench
Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3- phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-YL)BUTANAMIDE (cinnamoyl-phenylalanine-glnlactam-co-co-nh-benzyl)
Analyse Structure of human coronavirus NL63 main protease in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FV2
- Type
- protein
- Length
- 899 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.-
- UniProt
- P0C6X5
- Ligands
- D03
- Pockets
- 7 · best druggability 0.78
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.-) | protein | 301 | 25% helix, 29% strand | P0C6X5 |
| B, C | 3C-like proteinase (EC 3.4.22.-) | protein | 299 | 25% helix, 29% strand | P0C6X5 |
Ligands and binding sites
- D03 · (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.78 | 0.80 | 98 | empty |
| 2 | 1057 | 0.78 | 0.80 | 107 | D03 |
| 3 | 369 | 0.62 | 0.78 | 48 | empty |
| 4 | 386 | 0.61 | 0.77 | 47 | GOL |
| 5 | 250 | 0.50 | 0.75 | 28 | D03 |
Interfaces
3 interfaces between chains.
- B–C · 1330 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 240 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6FV2 · Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide… · 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 P0C6X5
- Elsewhere: RCSB PDB 6FV2 · PDBe 6FV2 · UniProt P0C6X5
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