4IUM: Papain-like protease 2

Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin. Determined by X-ray diffraction at 1.45 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Equine arteritis virus, Homo sapiens
Chains: 2
Atoms: 1,833
Mol. weight: 24.04 kDa
Ligands: ZN
Released: 13 Feb 2013

Explore 4IUM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IUM contains 11 α-helices and 15 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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	262	1	1
α-helix	270-277	8
β-strand	283-285	3	2
α-helix	290-292	3
β-strand	295	1	3
α-helix	296-305	10
β-strand	309-312	4	1
β-strand	324-329	6	1
β-strand	332-337	6	1
α-helix	347-351	5
α-helix	356-358	3
α-helix	362-368	7
α-helix	369-379	11
β-strand	384-386	3	2

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	56-59	4
β-strand	66-71	6	4
β-strand	74	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
papain-like protease 2	A	protein	142	Equine arteritis virus	P19811 (AlphaFold model)
Ubiquitin	B	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4IUM_1 papain-like protease 2 (chains A)
GYNPPGDGACGYRCLAFMNGATVVSAGCSSDLWCDDELAYRVFQLSPTFTVTIPGGRVCP
NAKYAMICDKQHWRVKRAKGVGLCLDESCFRGICNCQRMSGPPPAPVSAAVLDHILEAAT
FGNVRVVTPEGQGSSGHHHHHH

Sequence of entity 2 (B), FASTA

>4IUM_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells. van Kasteren, P.B., Bailey-Elkin, B.A., James, T.W. et al. Proc Natl Acad Sci U S A (2013) 110:E838-E847. DOI 10.1073/pnas.1218464110 · PubMed

Other PDB entries of the same protein (UniProt P19811 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MBM 2.0 Å, NSP4 proteinase from Equine Arteritis Virus
4N0N 2.0 Å, Crystal structure of Arterivirus nonstructural protein 10 (helicase)
4N0O 2.65 Å, Complex structure of Arterivirus nonstructural protein 10 (helicase) with DNA
5HBZ 3.1 Å, Structure of EAV NSP11 K170A mutant at 3.10A
5HC1 3.1 Å, Structure of EAV NSP11 H141A mutant at 3.10A
5F17 3.2 Å, Structure of EAV NSP11 K170A mutant at 3.19A
2L8K NMR Structure of the Arterivirus nonstructural protein 7 alpha (nsp7 alpha)

Browse structure collections

About this viewer

MolViewer shows 4IUM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.