Research workbench
2.26 a resolution structure of MERS 3CL protease in complex with inhibitor 7I
Analyse 2.26 a resolution structure of MERS 3CL protease in complex with inhibitor 7I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VH2
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A protein
- UniProt
- A0A1L2E0X0
- Ligands
- QZ4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A protein | protein | 299 | 24% helix, 29% strand | A0A1L2E0X0 |
| B | ORF1A protein | protein | 302 | 24% helix, 28% strand | A0A1L2E0X0 |
Ligands and binding sites
- QZ4 · 4,4-difluorocyclohexyl [(2S)-3-cyclohexyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.69 | 0.75 | 69 | empty |
| 2 | 355 | 0.58 | 0.76 | 46 | empty |
| 3 | 315 | 0.56 | 0.76 | 53 | empty |
| 4 | 219 | 0.52 | 0.77 | 31 | QZ4 |
| 5 | 197 | 0.51 | 0.77 | 27 | QZ4 |
Interfaces
1 interface between chains.
- A–B · 1069 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VH2 · 2.26 A resolution structure of MERS 3CL protease in complex with inhibitor 7i · 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 6VH2 · PDBe 6VH2 · UniProt A0A1L2E0X0
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