Research workbench
SARS-cov-2 main protease in complex with a cyclic peptide inhibitor
Analyse SARS-cov-2 main protease in complex with a cyclic peptide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RNW
- Type
- protein
- Length
- 1,255 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase; ACE-dty-leu-gln-tyr-ala-val-leu-arg-his-lys-arg-arg-glu- sec
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- ACE
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 3C-like proteinase (EC 3.4.22.69) | protein | 303 | 25% helix, 28% strand | P0DTD1 |
| B, C | 3C-like proteinase (EC 3.4.22.69) | protein | 304 | 26% helix, 29% strand | P0DTD1 |
| X | ACE-dty-leu-gln-tyr-ala-val-leu-arg-his-lys-arg-arg-glu- sec | protein | 8 | 0% helix, 0% strand | — |
| Y | ACE-dty-leu-gln-tyr-ala-val-leu-arg-his-lys-arg-arg-glu- sec | protein | 10 | 0% helix, 0% strand | — |
| Z | ACE-dty-leu-gln-tyr-ala-val-leu-arg-his-lys-arg-arg-glu- sec | protein | 13 | 0% helix, 8% strand | — |
| W | ACE-dty-leu-gln-tyr-ala-val-leu-arg-his-lys-arg-arg-glu- sec | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains C, X, A, Y, B, Z, D, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.80 | 0.83 | 101 | empty |
| 2 | 786 | 0.75 | 0.80 | 69 | empty |
| 3 | 891 | 0.74 | 0.78 | 71 | empty |
| 4 | 410 | 0.60 | 0.75 | 71 | empty |
| 5 | 265 | 0.51 | 0.74 | 51 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1533 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1508 Ų buried · 44 hydrogen bonds · protein-protein
- B–Z · 798 Ų buried · 20 hydrogen bonds · protein-protein
- D–W · 795 Ų buried · 13 hydrogen bonds · protein-protein
- A–Y · 705 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 d-amino, 4 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 7RNW · SARS-CoV-2 Main Protease in complex with a cyclic peptide 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 P0DTD1
- Elsewhere: RCSB PDB 7RNW · PDBe 7RNW · UniProt P0DTD1
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