Research workbench
Covalent complex of SARS-cov main protease with ethyl (4R)-4-({N-[(4- methoxy-1H-indol-2-YL)CARBONYL]-L-LEUCYL}AMINO)-5-[(3S)-2- oxopyrrolidin-3-YL]PENTANOATE
Analyse Covalent complex of SARS-cov main protease with ethyl (4R)-4-({N-[(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XHO
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0C6U8
- Ligands
- V34
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 29% strand | P0C6U8 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 294 | 25% helix, 30% strand | P0C6U8 |
Ligands and binding sites
- V34 · ethyl (2E,4S)-4-{[N-(4-methoxy-1H-indole-2-carbonyl)-L-leucyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.68 | 0.76 | 65 | EDO |
| 2 | 101 | 0.61 | 0.88 | 22 | empty |
| 3 | 384 | 0.55 | 0.74 | 52 | empty |
| 4 | 138 | 0.52 | 0.80 | 36 | empty |
| 5 | 196 | 0.51 | 0.77 | 25 | V34 |
Interfaces
1 interface between chains.
- A–B · 1016 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6XHO · Covalent complex of SARS-CoV main protease with ethyl… · 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 6XHO · PDBe 6XHO · UniProt P0C6U8
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