9W3O: Human rhinovirus A2 3C Protease

Crystal Structure of Human rhinovirus A2 3C Protease in Complex with a Broad-spectrum Inhibitor. Determined by X-ray diffraction at 1.76 Å resolution. Released 5 Aug 2026.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: rhinovirus A2
Chains: 2
Atoms: 2,883
Mol. weight: 41.25 kDa
Ligands: A1EYZ
Released: 5 Aug 2026

Explore 9W3O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W3O contains 15 α-helices and 30 β-strands across 2 chains. 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
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	97-104	8	1
β-strand	112-127	16	1
β-strand	130-138	9	1
β-strand	150-153	4	1
β-strand	156-164	9	1
β-strand	169-173	5	1
α-helix	174	1
α-helix	176-179	4

Chain B: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	15-20	6	3
β-strand	23-31	9	3
β-strand	32	1	4
β-strand	34-38	5	3
α-helix	39-41	3
β-strand	46-49	4	3
β-strand	52-63	12	3
β-strand	69-77	9	3
α-helix	81-82	2
β-strand	83	1	4
α-helix	84	1
α-helix	87-89	3
β-strand	97-104	8	5
β-strand	112-123	12	5
β-strand	126-127	2	6
β-strand	130-131	2	6
β-strand	135-138	4	5
α-helix	149	1
β-strand	150-153	4	5
β-strand	156-164	9	5
β-strand	169-173	5	5
α-helix	174	1
α-helix	176-179	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease 3C	A, B	protein	180	rhinovirus A2	P04936 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9W3O_1 Protease 3C (chains A, B)
GPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQVDGITTKVIDSY
DLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYPNCNLALLANQPEPTIINVGDVV
SYGNILLSGNQTARMLKYSYPTKSGYCGGVLYKIGQVLGIHVGGNGRDGFSAMLLRSYFT

Ligands and cofactors

ID	Name	Formula	Copies
A1EYZ	N-[(2S)-1-[(2S,3aS,7aS)-2-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3…	C36 H43 N5 O6	2

Primary citation

Harnessing AI, Structural Biology, and Medicinal Chemistry to Overcome Viral Diversity: Broad-Spectrum 3C/3CL Protease Inhibitors Effective Across Pisoniviricetes. Liu, L., Wang, J.L., Wang, S.H. et al. To be published.

Other PDB entries of the same protein (UniProt P04936 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FX6 1.45 Å, Novel inhibitors of human rhinovirus 3C protease
5FX5 1.7 Å, Novel inhibitors of human rhinovirus 3C protease
6FFN 1.75 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
1CQQ 1.85 Å, Type 2 rhinovirus 3C protease with AG7088 inhibitor
6FFS 1.86 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
2HRV 1.95 Å, 2A cysteine proteinase from human rhinovirus 2
1A3R 2.1 Å, FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2)…
7ARA 2.24 Å, Rhinovirus A2 2A protease in complex with zVAM.fmk
2XYA 2.4 Å, Non-covalent inhibtors of rhinovirus 3C protease.
1FPN 2.6 Å, Human rhinovirus serotype 2 (HRV2)
3TN9 3.0 Å, X-ray structure of the HRV2 empty capsid (B-particle)
3VDD 3.2 Å, Structure of HRV2 capsid complexed with antiviral compound BTA798

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