MolNFT v1 · #106219 · protein
X-ray structure of MERS-cov NSP5 protease bound with a designed inhibitor
4RSP · ORF1A protein: “X-ray structure of MERS-cov NSP5 protease bound with a designed inhibitor”. X-ray diffraction, 2 ligands (BOC, CEV), 2 pockets (best druggability 0.53). MolNFT v1 #106219 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RSP
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A protein; Peptide inhibitor
- UniProt
- V9TU12
- Ligands
- BOC, CEV
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF1A protein | protein | 304 | 24% helix, 29% strand | V9TU12 |
| B | Peptide inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · chains A, B
- CEV · Ethyl (4R)-4-amino-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate · ligand · chains A, B
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 | 257 | 0.53 | 0.76 | 40 | empty |
| 2 | 89 | 0.45 | 0.80 | 20 | CEV |
Interfaces
1 interface between chains.
- A–B · 348 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, oxidation).
Compared structures
- 4RSP · X-ray structure of MERS-CoV nsp5 protease bound with a designed 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 V9TU12
- Elsewhere: RCSB PDB 4RSP · PDBe 4RSP · UniProt V9TU12
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