MolNFT v1 · #133009 · protein
Pandda analysis group deposition SARS-cov-2 main protease fragment screen -- crystal structure of SARS-cov-2 main protease in complex with pg-cov-42 (mpro-X2052)
5RHE · 3C-like proteinase: “Pandda analysis group deposition SARS-cov-2 main protease fragment screen -- crystal structure of SARS-cov-2…”. X-ray diffraction, 1 ligand (UPD), 4 pockets (best druggability 0.51). MolNFT v1 #133009 on…
- PDB
- 5RHE
- Type
- protein
- Length
- 304 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- UPD
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- UPD · 1-acetyl-N-(6-methoxypyridin-3-yl)piperidine-4-carboxamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.51 | 0.77 | 27 | UPD, DMS |
| 2 | 87 | 0.48 | 0.82 | 19 | DMS |
| 3 | 83 | 0.32 | 0.74 | 15 | empty |
| 4 | 54 | 0.32 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5RHE · PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal… · 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 P0DTD1
- Elsewhere: RCSB PDB 5RHE · PDBe 5RHE · UniProt P0DTD1
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