Research workbench
Structure-based design, synthesis, evaluation of peptide-mimetic SARS 3CL protease inhibitors
Analyse Structure-based design, synthesis, evaluation of peptide-mimetic SARS 3CL… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ATW
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; Peptide ACE-thr-val-alc-his-H
- EC
- 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- ACE
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 29% strand | P0C6U8 |
| C, D | Peptide ACE-thr-val-alc-his-H | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.77 | 0.79 | 76 | empty |
| 2 | 240 | 0.56 | 0.78 | 36 | empty |
| 3 | 127 | 0.41 | 0.75 | 24 | empty |
| 4 | 113 | 0.36 | 0.74 | 26 | empty |
| 5 | 129 | 0.36 | 0.72 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1354 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 3ATW · Structure-Based Design, Synthesis, Evaluation of Peptide-mimetic SARS 3CL Protease… · 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 P0C6U8
- Elsewhere: RCSB PDB 3ATW · PDBe 3ATW · UniProt P0C6U8
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