Research workbench
1.55 a resolution structure of MERS 3CL protease in complex with inhibitor GC813
Analyse 1.55 a resolution structure of MERS 3CL protease in complex with inhibitor GC813 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKK
- Type
- protein
- Length
- 301 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A protein
- UniProt
- A0A1L2E0X0
- Ligands
- AW4, B3G, MG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A protein | protein | 301 | 24% helix, 28% strand | A0A1L2E0X0 |
Ligands and binding sites
- AW4 · (1S,2S)-2-[(N-{[2-(3-chlorophenyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains A
- B3G · (1R,2S)-2-[(N-{[2-(3-chlorophenyl)ethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.55 | 0.78 | 30 | AW4, B3G |
| 2 | 189 | 0.46 | 0.74 | 33 | PG4 |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5WKK · 1.55 A resolution structure of MERS 3CL protease in complex with inhibitor GC813 · 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 5WKK · PDBe 5WKK · UniProt A0A1L2E0X0
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