2Z9K: 3C-like proteinase

Complex structure of SARS-CoV 3C-like protease with JMF1600. Determined by X-ray diffraction at 1.85 Å resolution. Released 25 Dec 2007.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: SARS coronavirus
Chains: 2
Atoms: 5,533
Mol. weight: 68.32 kDa
Ligands: DOZ
Released: 25 Dec 2007

Explore 2Z9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Z9K contains 32 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: 15 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	47-50	4
α-helix	54-59	6
α-helix	63-65	3
β-strand	66-70	5	2
β-strand	73-75	3	2
β-strand	77-83	7	2
β-strand	86-91	6	2
β-strand	100-103	4	3
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
β-strand	199	1	4
α-helix	201-213	13
α-helix	227-234	8
α-helix	235-237	3
β-strand	239	1	4
α-helix	240-242	3
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	293-300	8

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
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	48-50	3
α-helix	54-58	5
α-helix	63-65	3
β-strand	66-70	5	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	100-103	4	1
β-strand	111-118	8	1
β-strand	121-129	9	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
β-strand	199	1	7
α-helix	201-213	13
α-helix	227-234	8
α-helix	235-237	3
β-strand	239	1	7
α-helix	240-242	3
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	SARS coronavirus	P0C6X7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2Z9K_1 3C-like proteinase (chains A, B)
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIR
KSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNG
SPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGK
FYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC
SGVTFQ

Ligands and cofactors

ID	Name	Formula	Copies
DOZ	(dimethylamino)(hydroxy)zinc'	C2 H7 N O Zn	2

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

Primary citation

Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors. Lee, C.C., Kuo, C.J., Hsu, M.F. et al. FEBS Lett (2007) 581:5454-5458. DOI 10.1016/j.febslet.2007.10.048 · 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,…

Browse structure collections

About this viewer

MolViewer shows 2Z9K 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.