4RNA: Papain-like protease

Crystal structure of PLpro from Middle East Respiratory Syndrome (MERS) coronavirus. Determined by X-ray diffraction at 1.79 Å resolution. Released 25 Mar 2015.

Method: X-ray diffraction
Resolution: 1.79 Å
Organism: Human betacoronavirus 2c EMC/2012
Chains: 1
Atoms: 2,745
Mol. weight: 36.5 kDa
Ligands: PO4, ZN
Released: 25 Mar 2015

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

Secondary structure: helices and β-sheets

4RNA contains 12 α-helices and 21 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: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
β-strand	16-21	6	1
α-helix	26-29	4
β-strand	33-35	3	1
β-strand	38-39	2	1
α-helix	44-45	2
α-helix	47-49	3
β-strand	53-56	4	1
α-helix	62-72	11
α-helix	79-90	12
β-strand	95-98	4	2
β-strand	101-104	4	2
α-helix	105-106	2
α-helix	111-120	10
β-strand	126-128	3	3
α-helix	131-141	11
α-helix	146-156	11
α-helix	166-174	9
β-strand	177-179	3	3
β-strand	184-191	8	4
β-strand	195-202	8	4
α-helix	203-207	5
β-strand	208-210	3	5
α-helix	215-219	5
β-strand	222-225	4	4
β-strand	231-240	10	4
β-strand	243-256	14	5
β-strand	265-270	6	5
β-strand	278-285	8	5
β-strand	288-292	5	5
β-strand	297-300	4	5
β-strand	302-313	12	5
β-strand	316-318	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
papain-like protease	A	protein	324	Human betacoronavirus 2c EMC/2012	K4LC41 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4RNA_1 papain-like protease (chains A)
GPQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLAD
NLTADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIM
TLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAE
LCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVE
HTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVS
KTSDWKCKVTDVLFPGQKYSSDCN

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4
ZN	Zinc ion	Zn	1

Primary citation

Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV. Lee, H., Lei, H., Santarsiero, B.D. et al. ACS Chem Biol (2015) 10:1456-1465. DOI 10.1021/cb500917m · PubMed

Other PDB entries of the same protein (UniProt K4LC41 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YNM 1.68 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppA
5YNF 1.79 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppA
5YNN 1.86 Å, Crystal structure of MERS-CoV nsp16/nsp10complex bound to sinefungin and m7GpppG
5YN6 1.95 Å, Crystal structure of MERS-CoV nsp10/nsp16 complex bound to SAM
5YNQ 1.96 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppG
5YN5 1.96 Å, Crystal structure of MERS-CoV nsp10/nsp16 complex
5YNO 1.96 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppA
5YN8 1.97 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH
5YNB 1.98 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to Sinefungin
5YNJ 2.04 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to m7GpppG
5YNI 2.07 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAM and m7GpppG
5YNP 2.27 Å, Crystal structure of MERS-CoV nsp16/nsp10 complex bound to sinefungin and m7GpppA

Browse structure collections

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