Research workbench
Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain
Analyse Structure of coronavirus main proteinase reveals combination of a chymotrypsin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LVO
- Type
- protein
- Length
- 1,798 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase, hydrolase domain
- UniProt
- Q9IW06
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Replicase, hydrolase domain | protein | 299 | 23% helix, 29% strand | Q9IW06 |
| B, C | Replicase, hydrolase domain | protein | 300 | 24% helix, 28% strand | Q9IW06 |
| D | Replicase, hydrolase domain | protein | 301 | 24% helix, 29% strand | Q9IW06 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 27 copies · chains A, B, C, D, E, F
- DIO · 1,4-diethylene dioxide · additive · 9 copies · chains A, B, C, D, E, F
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.77 | 0.79 | 109 | SO4 |
| 2 | 719 | 0.76 | 0.81 | 71 | empty |
| 3 | 706 | 0.75 | 0.81 | 69 | DIO, SO4 |
| 4 | 414 | 0.70 | 0.82 | 50 | DIO |
| 5 | 453 | 0.70 | 0.81 | 51 | DIO |
Interfaces
7 interfaces between chains.
- A–B · 1317 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1290 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 481 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 241 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1LVO · Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold 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 Q9IW06
- Elsewhere: RCSB PDB 1LVO · PDBe 1LVO · UniProt Q9IW06
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