Research workbench
Crystal structure of SARS COV2 main protease in complex with FSP006
Analyse Crystal structure of SARS COV2 main protease in complex with FSP006 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NT2
- Type
- protein
- Length
- 605 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
- P0DTC1
- Ligands
- URK, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 305 | 26% helix, 29% strand | P0DTC1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 300 | 26% helix, 30% strand | P0DTC1 |
Ligands and binding sites
- URK · [(1S)-2-[(2,3-dimethoxyphenyl)methylamino]-1-(4-nitrophenyl)-2-oxidanylidene-ethyl] prop-2-enoate · ligand · chains A, B
- CL · Chloride ion · ion · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.76 | 0.78 | 86 | CL |
| 2 | 57 | 0.71 | 0.98 | 24 | DMS |
| 3 | 457 | 0.65 | 0.78 | 75 | DMS |
| 4 | 173 | 0.49 | 0.77 | 30 | empty |
| 5 | 193 | 0.48 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1495 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7NT2 · Crystal structure of SARS CoV2 main protease in complex with FSP006 · 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 P0DTC1
- Elsewhere: RCSB PDB 7NT2 · PDBe 7NT2 · UniProt P0DTC1
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