7KQP: SARS-CoV-2 NSP3 macrodomain

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal form). Determined by X-ray diffraction at 0.88 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 0.88 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 2
Atoms: 3,604
Mol. weight: 36.92 kDa
Ligands: AR6
Released: 9 Dec 2020

Explore 7KQP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KQP contains 23 α-helices and 14 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: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9	1
β-strand	10-11	2	1
β-strand	16-20	5	1
α-helix	23-30	8
β-strand	34-39	6	1
α-helix	48-56	9
α-helix	60-72	13
α-helix	74-76	3
β-strand	80-84	5	1
β-strand	91-96	6	1
α-helix	100-102	3
α-helix	108-114	7
α-helix	115-118	4
β-strand	121-124	4	1
α-helix	136-146	11
β-strand	150-155	6	1
α-helix	158-165	8

Chain B: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9	1
β-strand	10-11	2	2
β-strand	16-20	5	2
α-helix	23-30	8
β-strand	34-38	5	2
α-helix	48-56	9
α-helix	60-72	13
α-helix	74-76	3
β-strand	80-84	5	2
β-strand	91-95	5	2
α-helix	100-102	3
α-helix	106-108	3
α-helix	109-114	6
α-helix	115-118	4
β-strand	121-124	4	2
α-helix	125-126	2
α-helix	130-132	3
α-helix	136-146	11
β-strand	150-155	6	2
α-helix	158-168	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 3	A, B	protein	169	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7KQP_1 Non-structural protein 3 (chains A, B)
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNA
MQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHE
VLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL

Ligands and cofactors

ID	Name	Formula	Copies
AR6	[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl[hydroxy-[…	C15 H23 N5 O14 P2	1

Primary citation

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Schuller, M., Correy, G.J., Gahbauer, S. et al. Sci Adv (2021) 7. DOI 10.1126/sciadv.abf8711 · 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…
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)
7TWR 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 8 (P43 crystal form)

Browse structure collections

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