- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.67 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.2: 5 residues within 4Å:- Chain A: M.6, F.8, D.295, R.298
- Chain B: S.123
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.295, B:S.123
1PE.9: 6 residues within 4Å:- Chain A: S.123
- Chain B: M.6, F.8, F.294, D.295, R.298
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:M.6, B:R.298, A:S.123
1PE.15: 9 residues within 4Å:- Chain A: Y.126, Q.127
- Chain B: F.3, R.4, K.5, W.207, E.288
- Ligands: PEG.4, PEG.16
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:R.4, B:K.5, B:E.288, A:Q.127, A:Q.127
- 9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.3: 7 residues within 4Å:- Chain A: G.15, M.17, W.31, G.71, N.95, P.96, K.97
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.95
PEG.4: 9 residues within 4Å:- Chain A: R.4, K.5, Y.126, Q.127
- Chain B: K.5, V.125, Y.126, Q.127
- Ligands: 1PE.15
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:A.7, B:Q.127, A:R.4, A:Q.127
- Water bridges: A:R.4
PEG.5: 5 residues within 4Å:- Chain A: F.3, W.207, A.211, N.214, L.286
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:F.3, A:F.3, A:N.214
- Water bridges: A:D.216
PEG.10: 2 residues within 4Å:- Chain B: T.24, T.25
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.25
PEG.11: 6 residues within 4Å:- Chain B: E.14, G.15, M.17, W.31, N.95, K.97
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.97
PEG.12: 1 residues within 4Å:- Chain B: N.214
No protein-ligand interaction detected (PLIP)PEG.13: 4 residues within 4Å:- Chain B: Y.37, Y.101, K.102, F.103
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:F.103
PEG.14: 6 residues within 4Å:- Chain A: F.3, R.4
- Chain B: K.5, E.288, D.289, E.290
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:R.4, B:K.5, B:E.288
- Water bridges: A:F.3
PEG.16: 4 residues within 4Å:- Chain A: E.290
- Chain B: F.3, R.4
- Ligands: 1PE.15
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.290
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.6: 3 residues within 4Å:- Chain A: S.62, N.63, H.64
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.62, A:S.62, A:N.63, A:N.63, A:H.64
- Salt bridges: A:H.64
PO4.7: 2 residues within 4Å:- Chain A: I.213, N.214
No protein-ligand interaction detected (PLIP)PO4.17: 3 residues within 4Å:- Chain B: S.62, N.63, H.64
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.63, B:N.63, B:H.64
- Salt bridges: B:H.64
PO4.18: 4 residues within 4Å:- Chain B: D.216, W.218, R.279, T.280
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:T.280
- Salt bridges: B:R.279
PO4.19: 2 residues within 4Å:- Chain B: Q.19, Q.69
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Q.19, B:Q.19, B:Q.69
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lee, J. et al., X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun (2022)
- Release Date
- 2022-09-21
- Peptides
- Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.67 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 5 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Lee, J. et al., X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun (2022)
- Release Date
- 2022-09-21
- Peptides
- Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B