Research workbench
1.70 a resolution structure of SARS-cov 3CL protease in complex with a deuterated GC376 alpha-ketoamide analog (compound 5)
Analyse 1.70 a resolution structure of SARS-cov 3CL protease in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0H
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1A
- EC
- 3.4.19.12, 3.4.22.-, 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- VR4, CL
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1A (EC 3.4.19.12, 3.4.22.-, 3.4.22.69) | protein | 298 | 26% helix, 30% strand | P0C6U8 |
| B | Replicase polyprotein 1A (EC 3.4.19.12, 3.4.22.-, 3.4.22.69) | protein | 300 | 26% helix, 30% strand | P0C6U8 |
Ligands and binding sites
- VR4 · N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy) carbonyl]-L-leucinamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains B
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 | 799 | 0.70 | 0.76 | 64 | empty |
| 2 | 276 | 0.58 | 0.78 | 49 | empty |
| 3 | 89 | 0.55 | 0.85 | 18 | empty |
| 4 | 219 | 0.52 | 0.77 | 27 | VR4 |
| 5 | 179 | 0.51 | 0.78 | 26 | VR4 |
Interfaces
1 interface between chains.
- A–B · 1026 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7K0H · 1.70 A resolution structure of SARS-CoV 3CL protease in complex with a deuterated GC376… · 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 7K0H · PDBe 7K0H · UniProt P0C6U8
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