Research workbench
Coronavirus main proteinase (3CLPRO) structure: basis for design of anti-SARS drugs
Analyse Coronavirus main proteinase (3CLPRO) structure: basis for design of anti-SARS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P9S
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB
- EC
- 3.4.24.-
- UniProt
- Q05002
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB (EC 3.4.24.-) | protein | 300 | 23% helix, 29% strand | Q05002 |
| B | Replicase polyprotein 1AB (EC 3.4.24.-) | protein | 299 | 24% helix, 29% strand | Q05002 |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.76 | 0.79 | 91 | empty |
| 2 | 273 | 0.67 | 0.83 | 47 | empty |
| 3 | 250 | 0.62 | 0.81 | 39 | empty |
| 4 | 410 | 0.59 | 0.75 | 55 | empty |
| 5 | 185 | 0.49 | 0.76 | 27 | DIO |
Interfaces
1 interface between chains.
- A–B · 1347 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1P9S · Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs · 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 Q05002
- Elsewhere: RCSB PDB 1P9S · PDBe 1P9S · UniProt Q05002
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