6XA9: SARS CoV-2 PLpro

SARS CoV-2 PLpro in complex with ISG15 C-terminal domain propargylamide. Determined by X-ray diffraction at 2.9 Å resolution. Released 17 Jun 2020.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Chains: 6
Atoms: 8,969
Mol. weight: 135.95 kDa
Ligands: ZN
Released: 17 Jun 2020

Explore 6XA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XA9 contains 47 α-helices and 84 β-strands across 6 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: 11 helices, 21 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
α-helix	44-47	4
α-helix	48-50	3
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	130-140	11
α-helix	145-155	11
α-helix	165-173	9
β-strand	176	1	3
β-strand	182-189	8	4
β-strand	193-200	8	4
α-helix	202-205	4
β-strand	206-208	3	5
α-helix	213-218	6
β-strand	220-223	4	4
β-strand	229-238	10	4
β-strand	241-254	14	5
β-strand	260-267	8	5
β-strand	270-278	9	5
β-strand	282-286	5	5
β-strand	289-293	5	5
β-strand	295-306	12	5
β-strand	309-311	3	4

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	82-87	6	6
β-strand	93-98	6	6
β-strand	103	1	7
α-helix	104-115	12
β-strand	122-126	5	6
β-strand	129-130	2	6
α-helix	131-132	2
β-strand	136	1	7
α-helix	137-140	4
β-strand	147-152	6	6
α-helix	153-154	2

Chain C: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	8
β-strand	17-22	6	8
α-helix	27-31	5
β-strand	34-36	3	8
β-strand	39-40	2	8
α-helix	44-47	4
α-helix	48-50	3
β-strand	54-57	4	8
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	9
β-strand	101-102	2	9
α-helix	111-120	10
β-strand	127	1	10
α-helix	130-140	11
α-helix	145-155	11
α-helix	165-174	10
β-strand	176	1	10
β-strand	182-189	8	11
β-strand	193-200	8	11
α-helix	201-204	4
β-strand	206-208	3	12
α-helix	213-218	6
β-strand	220-223	4	11
β-strand	229-238	10	11
β-strand	241-252	12	12
α-helix	253-254	2
β-strand	260-267	8	12
β-strand	270-278	9	12
β-strand	282-286	5	12
β-strand	289-293	5	12
β-strand	297-306	10	12
β-strand	309-311	3	11

Chains D and F: 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
α-helix	131-132	2
β-strand	136	1	14
α-helix	137-140	4
α-helix	142-143	2
β-strand	147-152	6	13

Chain E: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
β-strand	17-20	4	15
α-helix	27-31	5
β-strand	34-36	3	15
β-strand	39-40	2	15
α-helix	45-47	3
β-strand	54-57	4	15
α-helix	62-72	11
α-helix	79-90	12
β-strand	97-98	2	16
β-strand	101-102	2	16
α-helix	111-120	10
β-strand	127	1	17
α-helix	130-140	11
α-helix	145-155	11
α-helix	165-174	10
β-strand	176	1	17
β-strand	182-189	8	18
β-strand	193-200	8	18
α-helix	202-205	4
β-strand	206-208	3	19
α-helix	213-218	6
β-strand	220-223	4	18
β-strand	229-238	10	18
β-strand	241-254	14	19
β-strand	260-267	8	19
β-strand	270-278	9	19
β-strand	282-286	5	19
β-strand	289-293	5	19
β-strand	295-306	12	19
β-strand	309-311	3	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 3	A, C, E	protein	318	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)
ISG15 CTD-propargylamide	B, D, F	protein	80	Homo sapiens	P05161 (AlphaFold model)

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

>6XA9_1 Non-structural protein 3 (chains A, C, E)
GPREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV
LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL
LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN
LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ
ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK
GPITDVFYKENSYTTTIK

Sequence of entity 2 (B, D, F), FASTA

>6XA9_2 ISG15 CTD-propargylamide (chains B, D, F)
MDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDDLFWLTFEGKPLEDQLPL
GEYGLKPLSTVFMNLRLRGX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

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

Primary citation

Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. Klemm, T., Ebert, G., Calleja, D.J. et al. EMBO J (2020) 39:e106275-e106275. DOI 10.15252/embj.2020106275 · PubMed

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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