5TL6: SARS-CoV papain-like protease

Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain of human ISG15. Determined by X-ray diffraction at 2.62 Å resolution. Released 3 May 2017.

Method: X-ray diffraction
Resolution: 2.62 Å
Organisms: Human SARS coronavirus, Homo sapiens
Chains: 4
Atoms: 6,323
Mol. weight: 89.66 kDa
Ligands: ZN
Released: 3 May 2017

Explore 5TL6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TL6 contains 33 α-helices and 56 β-strands across 4 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	13
β-strand	93-98	6	13
β-strand	103	1	14
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	13
β-strand	129-130	2	13
β-strand	136	1	14
α-helix	137-140	4
α-helix	142-143	2
β-strand	147-152	6	13
α-helix	153-154	2

Chain B: 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	45-48	4
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	131-140	10
α-helix	146-155	10
α-helix	166-174	9
β-strand	177	1	3
β-strand	183-189	7	4
β-strand	195-201	7	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	261-268	8	5
β-strand	271-279	9	5
β-strand	283-287	5	5
β-strand	290-294	5	5
β-strand	297-307	11	5
β-strand	311-312	2	4

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	11
β-strand	93-98	6	11
β-strand	103	1	12
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	11
β-strand	129-131	3	11
α-helix	132	1
β-strand	136	1	12
α-helix	137-140	4
β-strand	147-152	6	11
α-helix	153-154	2

Chain D: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	6
β-strand	17-22	6	6
α-helix	28-31	4
β-strand	35-38	4	6
β-strand	40-41	2	6
α-helix	46-48	3
α-helix	49-51	3
β-strand	55-58	4	6
α-helix	67-73	7
α-helix	80-91	12
β-strand	98-99	2	7
β-strand	102-103	2	7
α-helix	112-121	10
β-strand	128	1	8
α-helix	131-142	12
α-helix	146-156	11
α-helix	166-175	10
β-strand	177	1	8
β-strand	183-190	8	9
β-strand	194-201	8	9
α-helix	203-206	4
β-strand	207-209	3	10
α-helix	214-219	6
β-strand	221-224	4	9
β-strand	230-239	10	9
β-strand	242-253	12	10
α-helix	254-255	2
β-strand	261-267	7	10
β-strand	272-279	8	10
β-strand	283-287	5	10
β-strand	290-294	5	10
β-strand	298-307	10	10
β-strand	310-312	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replicase polyprotein 1ab	B, D	protein	319	Human SARS coronavirus	P0C6X7 (AlphaFold model)
Ubiquitin-like protein ISG15	A, C	protein	79	Homo sapiens	P05161 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>5TL6_1 Replicase polyprotein 1ab (chains B, D)
MASMEVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFF
VLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSV
LLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHA
NLESAKRVLNVVCKHCGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPCVCGRDATQYLVQ
QESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEY
KGPVTDVFYKETSYTTTIK

Sequence of entity 2 (A, C), FASTA

>5TL6_2 Ubiquitin-like protein ISG15 (chains A, C)
MEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPLG
EYGLKPLSTVFMNLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species. Daczkowski, C.M., Dzimianski, J.V., Clasman, J.R. et al. J Mol Biol (2017) 429:1661-1683. DOI 10.1016/j.jmb.2017.04.011 · PubMed

Other PDB entries of the same protein (UniProt P0C6X7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ACF 1.4 Å, NMR structure of SARS-CoV non-structural protein NSP3A (SARS1) from SARS coronavirus
6W79 1.46 Å, Structure of SARS-CoV main protease bound to potent broad-spectrum non-covalent…
6WCO 1.48 Å, Structure of SARS main protease bound to inhibitor X47
5C5O 1.5 Å, Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type…
8CB3 1.57 Å, SARS-CoV Macro domain complexed with 3-(N-morpholino)propanesulfonic acid
3TNT 1.59 Å, Crystal structure of SARS coronavirus main protease complexed with an alpha,…
4TWY 1.6 Å, Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor
7FA1 1.6 Å, Crystal Structure of N-terminus of the non-structural protein 2 from SARS coronavirus
5N19 1.62 Å, Structure of SARS coronavirus main protease in complex with the alpha-ketoamide…
2ZU5 1.65 Å, complex structure of SARS-CoV 3CL protease with TG-0205486
8UFM 1.65 Å, Crystal Structure of L516C/Y647C Mutant of SARS-Unique Domain (SUD) from SARS-CoV-2
3SZN 1.69 Å, Crystal structure of SARS coronavirus main protease complexed with an alpha,…

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