5S74

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain

PDB DOI: https://doi.org/10.2210/pdb5S74/pdb
Deposition Group: G_1002182 (ground state) ExploreG_1002182

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

Deposited: 2020-11-23 Released: 2021-01-13
Deposition Author(s): Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunnet, L., Gorrie-Stone, T.J., Powell, A.J., Krojer, T., Skyner, R., Thompson, W., Ahel, I., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.96 Å
R-Value Free: 0.185
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation

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

Literature

PanDDA analysis group deposition of ground-state model of SARS-CoV-2 Nsp3 macrodomain

Fearon, D., Schuller, M., Rangel, V.L., Douangamath, A., Rack, J.G.M., Zhu, K., Aimon, A., Brandao-Neto, J., Dias, A., Dunnet, L., Gorrie-Stone, T.J., Powell, A.J., Krojer, T., Skyner, R., Thompson, W., Ahel, I., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 36.73 kDa
Atom Count: 2,967
Modelled Residue Count: 334
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B	169	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A] D [auth A] E [auth B] F [auth B] G [auth B] C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.96 Å
R-Value Free: 0.185
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.877	α = 90
b = 87.877	β = 90
c = 38.634	γ = 90

Software Package:

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

Structure Validation

Entry History

Deposition Data

Released Date: 2021-01-13

Deposition Author(s):

Douangamath, A.

Brandao-Neto, J.

Gorrie-Stone, T.J.

Revision History (Full details and data files)

Version 1.0: 2021-01-13
Type: Initial release
Version 1.1: 2021-01-27
Changes: Structure summary
Version 1.2: 2024-03-06
Changes: Data collection, Database references

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.