Research workbench
2.05 a resolution structure of MERS 3CL protease in complex with inhibitor 6B
Analyse 2.05 a resolution structure of MERS 3CL protease in complex with inhibitor 6B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGY
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A protein
- UniProt
- A0A1L2E0X0
- Ligands
- QZJ
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A protein | protein | 297 | 25% helix, 28% strand | A0A1L2E0X0 |
| B | ORF1A protein | protein | 298 | 24% helix, 28% strand | A0A1L2E0X0 |
Ligands and binding sites
- QZJ · N~2~-{[(trans-4-ethylcyclohexyl)oxy]carbonyl}-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.76 | 0.78 | 114 | empty |
| 2 | 233 | 0.54 | 0.77 | 30 | QZJ |
| 3 | 184 | 0.50 | 0.77 | 26 | QZJ |
Interfaces
1 interface between chains.
- A–B · 1091 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VGY · 2.05 A resolution structure of MERS 3CL protease in complex with inhibitor 6b · 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 A0A1L2E0X0
- Elsewhere: RCSB PDB 6VGY · PDBe 6VGY · UniProt A0A1L2E0X0
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