5Y3E: SARS coronavirus papain-like protease

Crystal structure of SARS coronavirus papain-like protease in complex with glycerol. Determined by X-ray diffraction at 1.65 Å resolution. Released 10 Jan 2018.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Human SARS coronavirus
Chains: 1
Atoms: 2,901
Mol. weight: 36.92 kDa
Ligands: ZN
Released: 10 Jan 2018

Explore 5Y3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y3E contains 11 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: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	1
β-strand	18-23	6	1
α-helix	28-32	5
β-strand	35-37	3	1
β-strand	40-41	2	1
α-helix	46-47	2
α-helix	49-51	3
β-strand	55-58	4	1
α-helix	63-73	11
α-helix	80-91	12
β-strand	98-99	2	2
β-strand	102-103	2	2
α-helix	112-121	10
β-strand	128	1	3
α-helix	131-141	11
α-helix	146-155	10
α-helix	166-174	9
β-strand	177	1	3
β-strand	183-190	8	4
β-strand	194-201	8	4
α-helix	203-206	4
β-strand	207-209	3	5
α-helix	214-219	6
β-strand	221-224	4	4
β-strand	230-239	10	4
β-strand	242-254	13	5
β-strand	261-267	7	5
β-strand	272-279	8	5
β-strand	283-287	5	5
β-strand	290-294	5	5
β-strand	297-307	11	5
β-strand	310-312	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replicase polyprotein 1a	A	protein	323	Human SARS coronavirus	P0C6U8

Sequence of entity 1 (A), FASTA

>5Y3E_1 Replicase polyprotein 1a (chains A)
MEVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLP
SDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLA
LQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLE
SAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQQES
SFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGP
VTDVFYKETSYTTTILEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes. Lin, M.H., Moses, D.C., Hsieh, C.H. et al. Antiviral Res (2017) 150:155-163. DOI 10.1016/j.antiviral.2017.12.015 · PubMed

Other PDB entries of the same protein (UniProt P0C6U8), best resolution first:

6XHN 1.38 Å, Covalent complex of SARS-CoV main protease with 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)…
4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
6XHO 1.45 Å, Covalent complex of SARS-CoV main protease with ethyl (4R)-4-({N-[(4-methoxy-1H-indol-2-y…
6XHL 1.47 Å, Covalent complex of SARS-CoV main protease with N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)…
4MDS 1.6 Å, Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as…
2H2Z 1.6 Å, Crystal structure of SARS-CoV main protease with authentic N and C-termini
7LMG 1.6 Å, SARS-CoV-1 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-2-(1H-benzo[d][1,2,3]tri…
7RC1 1.63 Å, X-ray Structure of SARS-CoV main protease covalently modified by compound GRL-0686
5Y3Q 1.65 Å, Crystal structure of SARS coronavirus papain-like protease conjugated with…
6W2A 1.65 Å, 1.65 A resolution structure of SARS-CoV 3CL protease in complex with inhibitor 7j
7LMJ 1.69 Å, SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N…
2DUC 1.7 Å, Crystal structure of SARS coronavirus main proteinase(3CLPRO)

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