5C5O: 3C-like proteinase

Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (S,R)-N-decalin type inhibitor. Determined by X-ray diffraction at 1.5 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Human SARS coronavirus
Chains: 2
Atoms: 5,161
Mol. weight: 68.54 kDa
Ligands: SDJ
Released: 22 Jun 2016

Explore 5C5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C5O contains 34 α-helices and 40 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: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
α-helix	8-9	2
α-helix	11-14	4
β-strand	17-22	6	2
β-strand	25-32	8	2
β-strand	35-39	5	2
α-helix	40-43	4
α-helix	46-50	5
α-helix	54-59	6
α-helix	63-65	3
β-strand	67-70	4	2
β-strand	73-75	3	2
β-strand	77-83	7	2
β-strand	86-91	6	2
α-helix	98-99	2
β-strand	101-103	3	3
α-helix	106-107	2
β-strand	111-118	8	3
β-strand	121-129	9	3
β-strand	136	1	3
β-strand	148-153	6	3
β-strand	156-166	11	3
β-strand	172-175	4	3
α-helix	180	1
β-strand	181	1	3
α-helix	193-197	5
β-strand	199	1	4
α-helix	201-213	13
α-helix	227-236	10
β-strand	239	1	4
α-helix	240-241	2
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	5
β-strand	284	1	5
α-helix	293-299	7

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	3
α-helix	8-9	2
α-helix	11-14	4
β-strand	17-22	6	6
β-strand	25-32	8	6
β-strand	35-39	5	6
α-helix	40-43	4
α-helix	46-50	5
α-helix	54-59	6
α-helix	63-65	3
β-strand	67-70	4	6
β-strand	73-75	3	6
β-strand	77-83	7	6
β-strand	86-91	6	6
α-helix	98-99	2
β-strand	101-103	3	1
α-helix	106-107	2
β-strand	111-118	8	1
β-strand	121-130	10	1
β-strand	136	1	1
β-strand	148-153	6	1
β-strand	156-166	11	1
β-strand	172-175	4	1
α-helix	180	1
β-strand	181	1	1
α-helix	194-197	4
β-strand	199	1	7
α-helix	201-213	13
α-helix	227-236	10
β-strand	239	1	7
α-helix	240-243	4
α-helix	244-249	6
α-helix	251-257	7
α-helix	261-274	14
β-strand	281	1	8
β-strand	284	1	8
α-helix	293-299	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3C-like proteinase	A, B	protein	306	Human SARS coronavirus	P0C6X7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5C5O_1 3C-like proteinase (chains A, B)
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR
KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG
SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK
FYGPFVDIQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC
SGVTFQ

Ligands and cofactors

ID	Name	Formula	Copies
SDJ	(2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydrois…	C25 H35 N5 O2	2

Primary citation

Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors. Shimamoto, Y., Hattori, H., Kobayashi, K. et al. To be published.

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
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,…
5C5N 1.69 Å, Structure of SARS-3CL protease complex with a phenyl-beta-alanyl (R,S)-N-decalin type…

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