Research workbench
2.20 a resolution structure of MERS 3CL protease in complex with inhibitor 7J
Analyse 2.20 a resolution structure of MERS 3CL protease in complex with inhibitor 7J in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VH3
- Type
- protein
- Length
- 599 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A protein
- UniProt
- A0A1L2E0X0
- Ligands
- QYS
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A protein | protein | 300 | 24% helix, 29% strand | A0A1L2E0X0 |
| B | ORF1A protein | protein | 299 | 26% helix, 29% strand | A0A1L2E0X0 |
Ligands and binding sites
- QYS · (1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl) methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.70 | 0.76 | 70 | empty |
| 2 | 345 | 0.59 | 0.77 | 46 | empty |
| 3 | 276 | 0.55 | 0.76 | 42 | empty |
| 4 | 191 | 0.51 | 0.77 | 29 | QYS |
| 5 | 190 | 0.49 | 0.76 | 26 | QYS |
Interfaces
1 interface between chains.
- A–B · 985 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VH3 · 2.20 A resolution structure of MERS 3CL protease in complex with inhibitor 7j · 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 6VH3 · PDBe 6VH3 · UniProt A0A1L2E0X0
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