Research workbench
2.25 A resolution structure of MERS 3CL protease in complex with inhibitor 6d
Analyse 2.25 A resolution structure of MERS 3CL protease in complex with inhibitor 6d in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGZ
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Middle East respiratory syndrome-related coronavirus
- Molecule
- Orf1a protein
- UniProt
- A0A1L2E0X0
- Ligands
- QZG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.25 · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orf1a protein | protein | 296 | 25% helix, 28% strand | A0A1L2E0X0 |
| B | Orf1a protein | protein | 298 | 24% helix, 28% strand | A0A1L2E0X0 |
Ligands and binding sites
- QZG · N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[trans-4-(propan-2-yl) cyclohexyl]oxy}carbonyl)-L-leucinamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.74 | 0.78 | 97 | empty |
| 2 | 280 | 0.54 | 0.75 | 39 | empty |
| 3 | 223 | 0.53 | 0.77 | 31 | QZG |
| 4 | 206 | 0.53 | 0.78 | 31 | QZG |
Interfaces
1 interface between chains.
- A–B · 1057 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VGZ · 2.25 a resolution structure of MERS 3CL protease in complex with inhibitor 6D · 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 6VGZ · PDBe 6VGZ · UniProt A0A1L2E0X0
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