Research workbench
1.95 a resolution structure of MERS 3CL protease in complex with inhibitor 6G
Analyse 1.95 a resolution structure of MERS 3CL protease in complex with inhibitor 6G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VH0
- 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
- QZD
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A protein | protein | 297 | 26% helix, 28% strand | A0A1L2E0X0 |
| B | ORF1A protein | protein | 298 | 25% helix, 28% strand | A0A1L2E0X0 |
Ligands and binding sites
- QZD · N~2~-{[(5-ethyl-1,3-dioxan-5-yl)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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.72 | 0.75 | 67 | empty |
| 2 | 335 | 0.57 | 0.76 | 54 | empty |
| 3 | 250 | 0.53 | 0.76 | 37 | empty |
| 4 | 190 | 0.52 | 0.78 | 25 | QZD |
| 5 | 210 | 0.51 | 0.76 | 30 | QZD |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VH0 · 1.95 A resolution structure of MERS 3CL protease in complex with inhibitor 6g · 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 6VH0 · PDBe 6VH0 · UniProt A0A1L2E0X0
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