6W9C: Papain-like protease of SARS CoV-2

The crystal structure of papain-like protease of SARS CoV-2. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 7,371
Mol. weight: 107.81 kDa
Ligands: ZN
Released: 1 Apr 2020

Explore 6W9C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W9C contains 30 α-helices and 69 β-strands across 3 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: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-22	6	1
α-helix	27-31	5
β-strand	34-36	3	1
β-strand	39-40	2	1
β-strand	54-57	4	1
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	2
β-strand	101-102	2	2
α-helix	111-120	10
β-strand	127	1	3
α-helix	130-141	12
α-helix	145-154	10
α-helix	165-174	10
β-strand	176	1	3
β-strand	182-188	7	4
β-strand	189	1	5
β-strand	193	1	5
β-strand	196-200	5	4
α-helix	201-204	4
β-strand	206-208	3	6
α-helix	213-218	6
β-strand	220-223	4	4
β-strand	229-238	10	4
β-strand	241-253	13	6
α-helix	254	1
β-strand	260-265	6	6
β-strand	272-278	7	6
β-strand	282-286	5	6
β-strand	289-293	5	6
β-strand	296-306	11	6
β-strand	309-311	3	4

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	7
β-strand	17-22	6	7
α-helix	27-31	5
β-strand	34-36	3	7
β-strand	39-40	2	7
β-strand	54-57	4	7
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	8
β-strand	101-102	2	8
α-helix	111-120	10
β-strand	127	1	9
α-helix	130-141	12
α-helix	145-154	10
α-helix	165-174	10
β-strand	176	1	9
β-strand	182-188	7	10
β-strand	189	1	11
β-strand	193	1	11
β-strand	196-200	5	10
α-helix	201-204	4
β-strand	206-208	3	12
α-helix	213-218	6
β-strand	220-222	3	10
β-strand	230-238	9	10
β-strand	241-253	13	12
α-helix	254	1
β-strand	260-265	6	12
β-strand	272-278	7	12
β-strand	282-286	5	12
β-strand	289-293	5	12
β-strand	296-306	11	12
β-strand	310-311	2	10

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	13
β-strand	17-21	5	13
α-helix	27-31	5
β-strand	34-36	3	13
β-strand	39-40	2	13
β-strand	54-57	4	13
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	14
β-strand	101-102	2	14
α-helix	111-120	10
β-strand	127	1	15
α-helix	130-141	12
α-helix	145-154	10
α-helix	165-174	10
β-strand	176	1	15
β-strand	182-188	7	16
β-strand	189	1	17
β-strand	193	1	17
β-strand	196-200	5	16
α-helix	201-204	4
β-strand	206-208	3	18
α-helix	213-218	6
β-strand	220-223	4	16
β-strand	229-238	10	16
β-strand	241-253	13	18
α-helix	254	1
β-strand	260-265	6	18
β-strand	272-278	7	18
β-strand	282-286	5	18
β-strand	289-293	5	18
β-strand	296-306	11	18
β-strand	309-311	3	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 3	A, B, C	protein	317	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6W9C_1 Non-structural protein 3 (chains A, B, C)
EVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPN
DDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTL
QQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDS
CKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESP
FVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPI
TDVFYKENSYTTTIKAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

The crystal structure of papain-like protease of SARS CoV-2. Osipiuk, J., Jedrzejczak, R., Tesar, C. et al. To be published.

Other PDB entries of the same protein (UniProt P0DTD1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

44PS 0.77 Å, 6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
7KR0 0.77 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
9CY0 0.8 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4206
7TX0 0.84 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43…
7KQO 0.85 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)
7HCO 0.87 Å, PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in…
7KQP 0.88 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal…
7TWJ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 4 (P43 crystal form)
7TWN 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 5 (P43 crystal form)
7TWO 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)
7TWP 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 7 (P43 crystal form)
7TWQ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 9 (P43 crystal form)

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6W9C is part of these collections:

SARS-CoV-2 and COVID-19

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