7ARA: Rhinovirus A2 2A protease

Rhinovirus A2 2A protease in complex with zVAM.fmk. Determined by X-ray diffraction at 2.24 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Human rhinovirus 2
Chains: 2
Atoms: 2,277
Mol. weight: 33.49 kDa
Ligands: S7N, ZN, S7Q
Released: 28 Jul 2021

Explore 7ARA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ARA contains 5 α-helices and 21 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-16	10	1
α-helix	24-26	3
β-strand	29-31	3	1
β-strand	36-46	11	1
β-strand	56-61	6	2
β-strand	66-71	6	2
β-strand	72-79	8	3
β-strand	90-98	9	3
β-strand	109-111	3	2
β-strand	116-119	4	2
β-strand	120-123	4	3
β-strand	127-131	5	3
α-helix	133-136	4

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-16	10	4
β-strand	29-31	3	4
α-helix	32-34	3
β-strand	36-46	11	4
β-strand	56-61	6	5
α-helix	62-64	3
β-strand	66-71	6	5
β-strand	73-80	8	5
β-strand	89-97	9	5
β-strand	109-111	3	5
β-strand	116-124	9	5
β-strand	127-132	6	5
α-helix	133-136	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2A protease	A, B	protein	142	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7ARA_1 2A protease (chains A, B)
GPSDMYVHVGNLIYRNLHLFNSEMHESILVSYSSDLIIYRTNTVGDDYIPSCDCTQATYY
CKHKNRYFPITVTSHDWYEIQESEYYPKHIQYNLLIGEGPCEPGDCGGKLLCKHGVIGIV
TAGGDNHVAFIDLRHFHCAEEQ

Ligands and cofactors

ID	Name	Formula	Copies
S7N	(phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-…	C22 H33 N3 O5 S	1
ZN	Zinc ion	Zn	2
S7Q	(phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-…	C22 H33 N3 O5 S	1

Primary citation

Defining substrate selection by rhinoviral 2A proteinase through its crystal structure with the inhibitor zVAM.fmk. Deutschmann-Olek, K.M., Yue, W.W., Bezerra, G.A. et al. Virology (2021) 562:128-141. DOI 10.1016/j.virol.2021.07.008 · PubMed

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…
9W3O 1.76 Å, Crystal Structure of Human rhinovirus A2 3C Protease in Complex with a Broad-spectrum…
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)…
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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