6YWL

Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose

PDB DOI: https://doi.org/10.2210/pdb6YWL/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-29 Released: 2020-05-06
Deposition Author(s): Schroeder, M., Ni, X., Olieric, V., Sharpe, E.M., Wojdyla, J.A., Wang, M., Knapp, S., Chaikuad, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.223
R-Value Work: 0.189
R-Value Observed: 0.191

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain.

Ni, X., Schroder, M., Olieric, V., Sharpe, M.E., Hernandez-Olmos, V., Proschak, E., Merk, D., Knapp, S., Chaikuad, A.

(2021) ACS Med Chem Lett 12: 603-609

PubMed: 33850605 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.0c00684
Primary Citation of Related Structures:
6YWK, 6YWL, 6YWM, 7BF3, 7BF4, 7BF5, 7BF6

PubMed Abstract:
The nsP3 macrodomain is a conserved protein interaction module that plays essential regulatory roles in the host immune response by recognizing and removing posttranslational ADP-ribosylation sites during SARS-CoV-2 infection. Thus targeting this protein domain may offer a therapeutic strategy to combat current and future virus pandemics. To assist inhibitor development efforts, we report here a comprehensive set of macrodomain crystal structures complexed with diverse naturally occurring nucleotides, small molecules, and nucleotide analogues including GS-441524 and its phosphorylated analogue, active metabolites of remdesivir. The presented data strengthen our understanding of the SARS-CoV-2 macrodomain structural plasticity and provide chemical starting points for future inhibitor development.

Organizational Affiliation

Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 97.1 kDa
Atom Count: 6,900
Modelled Residue Count: 857
Deposited Residue Count: 865
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NSP3 macrodomain	A, B, C, D, E	173	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APR (Subject of Investigation/LOI) Query on APR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E]	F [auth A], M [auth B], P [auth C], T [auth D], X [auth E]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], Z [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain Y [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain Y [auth E]	Q [auth C], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain Y [auth E] Interactions & Density Focus chain Q [auth C] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.223
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.395	α = 90
b = 111.922	β = 90
c = 195.333	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description