8S6F: Protease 3C

A Structural Investigation of the Interaction between a GC-376-Based Peptidomimetic PROTAC and Its Precursor with the Viral Main Protease of Coxsackievirus B3. Determined by X-ray diffraction at 1.93 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 1.93 Å
Organism: Coxsackievirus B3
Chains: 1
Atoms: 1,496
Mol. weight: 20.39 kDa
Ligands: VQR
Released: 4 Dec 2024

Explore 8S6F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S6F contains 7 α-helices and 17 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	15-20	6	1
β-strand	23-31	9	1
β-strand	32	1	2
β-strand	34-38	5	1
α-helix	39-41	3
β-strand	46-49	4	1
β-strand	52-63	12	1
β-strand	69-77	9	1
α-helix	82	1
β-strand	83	1	2
α-helix	84	1
α-helix	87-89	3
β-strand	90	1	1
β-strand	91	1	3
β-strand	97-104	8	1
β-strand	112-127	16	1
β-strand	130-138	9	1
α-helix	149	1
β-strand	150-153	4	1
β-strand	156-163	8	1
β-strand	169-173	5	1
β-strand	175	1	3
α-helix	176-179	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease 3C	A	protein	180	Coxsackievirus B3	P03313

Sequence of entity 1 (A), FASTA

>8S6F_1 Protease 3C (chains A)
GPAFEFAVAMMKRNSSTVKTEYGEFTMLGIYDRWAVLPRHAKPGPTILMNDQEVGVLDAK
ELVDKDGTNLELTLLKLNRNEKFRDIRGFLAKEEVEVNEAVLAINTSKFPNMYIPVGQVT
EYGFLNLGGTPTKRMLMYNFPTRAGQCGGVLMSTGKVLGIHVGGNGHQGFSAALLKHYFN

Ligands and cofactors

ID	Name	Formula	Copies
VQR	methyl (4~{S})-4-[[(2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]ami…	C24 H35 N3 O6	1

Primary citation

A Structural Investigation of the Interaction between a GC-376-Based Peptidomimetic PROTAC and Its Precursor with the Viral Main Protease of Coxsackievirus B3. De Santis, A., Grifagni, D., Orsetti, A. et al. Biomolecules (2024) 14. DOI 10.3390/biom14101260 · PubMed

Other PDB entries of the same protein (UniProt P03313), best resolution first:

7W0Q 1.1 Å, TRIM7 in complex with C-terminal peptide of 2C
2ZU1 1.38 Å, crystal structure of CVB3 3C protease mutant C147A
7W0S 1.4 Å, TRIM7 in complex with C-terminal peptide of 2C
6S3A 1.52 Å, Coxsackie B3 2C protein in complex with S-Fluoxetine
7W0T 1.57 Å, TRIM7 in complex with C-terminal peptide of 2C
7QUW 1.65 Å, CVB3-3Cpro in complex with inhibitor MG-78
2ZTX 1.72 Å, Complex structure of CVB3 3C protease with EPDTC
2ZTY 1.72 Å, crystal structure of 3C protease from CVB3 in space group C2
2ZU3 1.75 Å, Complex structure of CVB3 3C protease with TG-0204998
4WFZ 1.8 Å, Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase - NaCl Crystal Form
4WFX 1.81 Å, Coxsackievirus B3 Polymerase - F232L Mutant - NaCl Crystal Form
6T3W 1.82 Å, Coxsackie B3 2C protein in complex with S-Fluoxetine

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