6Z6I | pdb_00006z6i

SARS-CoV-2 Macrodomain in complex with ADP-HPD

PDB DOI: https://doi.org/10.2210/pdb6Z6I/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-05-28 Released: 2020-12-02
Deposition Author(s): Zorzini, V., Rack, J., Ahel, I.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.279 (Depositor), 0.283 (DCC)
R-Value Work:
0.229 (Depositor), 0.239 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.

Rack, J.G.M., Zorzini, V., Zhu, Z., Schuller, M., Ahel, D., Ahel, I.

(2020) Open Biol 10: 200237-200237

PubMed: 33202171 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1098/rsob.200237
Primary Citation Related Structures:
6Z5T, 6Z6I, 6Z72

PubMed Abstract:
Viral macrodomains possess the ability to counteract host ADP-ribosylation, a post-translational modification implicated in the creation of an antiviral environment via immune response regulation. This brought them into focus as promising therapeutic targets, albeit the close homology to some of the human macrodomains raised concerns regarding potential cross-reactivity and adverse effects for the host. Here, we evaluate the structure and function of the macrodomain of SARS-CoV-2, the causative agent of COVID-19. We show that it can antagonize ADP-ribosylation by PARP14, a cellular (ADP-ribosyl)transferase necessary for the restriction of coronaviral infections. Furthermore, our structural studies together with ligand modelling revealed the structural basis for poly(ADP-ribose) binding and hydrolysis, an emerging new aspect of viral macrodomain biology. These new insights were used in an extensive evolutionary analysis aimed at evaluating the druggability of viral macrodomains not only from the Coronaviridae but also Togaviridae and Iridoviridae genera (causing diseases such as Chikungunya and infectious spleen and kidney necrosis virus disease, respectively). We found that they contain conserved features, distinct from their human counterparts, which may be exploited during drug design.

Organizational Affiliation

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.

Macromolecule Content

Total Structure Weight: 80.85 kDa
Atom Count: 6,354
Modeled Residue Count: 692
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B, C, D	176	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1R (Subject of Investigation/LOI) Query on A1R Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth C]	CA [auth D] E [auth A] J [auth A] M [auth B] R [auth C] CA [auth D], E [auth A], J [auth A], M [auth B], R [auth C], X [auth C]	5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE C₁₅ H₂₄ N₆ O₁₂ P₂ NDQDTBCXPOIQGT-UHNJQBFTSA-N		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain X [auth C]
MPO Query on MPO Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth C]	DA [auth D], H [auth A], N [auth B], S [auth C], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	EA [auth D] F [auth A] FA [auth D] G [auth A] GA [auth D] EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], HA [auth D], I [auth A], IA [auth D], JA [auth D], P [auth B], T [auth C], U [auth C], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] K [auth A] KA [auth D] L [auth A] AA [auth C], BA [auth C], K [auth A], KA [auth D], L [auth A], LA [auth D], Q [auth B], Y [auth C], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]