Research workbench
X-ray structure of MERS-cov NSP5 protease bound with a non-covalent inhibitor
Analyse X-ray structure of MERS-cov NSP5 protease bound with a non-covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YLU
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A protein
- UniProt
- A0A0A7E693
- Ligands
- R30
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ORF1A protein | protein | 304 | 25% helix, 30% strand | A0A0A7E693 |
| B, C | ORF1A protein | protein | 302 | 25% helix, 29% strand | A0A0A7E693 |
Ligands and binding sites
- R30 · N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}propanamide · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.79 | 0.81 | 67 | ACT |
| 2 | 1004 | 0.78 | 0.80 | 68 | ACT |
| 3 | 710 | 0.67 | 0.75 | 80 | empty |
| 4 | 732 | 0.67 | 0.75 | 83 | empty |
| 5 | 318 | 0.59 | 0.77 | 46 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1373 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1326 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4YLU · X-ray structure of MERS-CoV nsp5 protease bound with a non-covalent inhibitor · 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 A0A0A7E693
- Elsewhere: RCSB PDB 4YLU · PDBe 4YLU · UniProt A0A0A7E693
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