8SH8 | pdb_00008sh8

Crystal structure of SARS-CoV-2 NSP3 macrodomain Asn40Asp mutant in complex with ADP-ribose (P43 crystal form)

PDB DOI: https://doi.org/10.2210/pdb8SH8/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-13 Released: 2024-05-01
Deposition Author(s): Correy, G.J., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.90 Å
R-Value Free:
0.123 (Depositor), 0.123 (DCC)
R-Value Work:
0.114 (Depositor), 0.115 (DCC)
R-Value Observed:
0.115 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of SARS-CoV-2 NSP3 macrodomain Asn40Asp mutant in complex with ADP-ribose (P43 crystal form)

Correy, G.J., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 36.92 kDa
Atom Count: 3,322
Modeled Residue Count: 338
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 (Subject of Investigation/LOI) Query on AR6 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.90 Å
R-Value Free: 0.123 (Depositor), 0.123 (DCC)
R-Value Work: 0.114 (Depositor), 0.115 (DCC)
R-Value Observed: 0.115 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.069	α = 90
b = 88.069	β = 90
c = 39.071	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110

Revision History (Full details and data files)

Version 1.0: 2024-05-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.