7DAT | pdb_00007dat

The crystal structure of COVID-19 main protease treated by AF

PDB DOI: https://doi.org/10.2210/pdb7DAT/pdb

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

Deposited: 2020-10-18 Released: 2021-11-03
Deposition Author(s): He, Z.S., He, B., Cao, P., Jiang, H.D., Gong, Y., Gao, X.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.194 (Depositor), 0.195 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7DAT

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8B0S

Literature

A comparison of Remdesivir versus gold cluster in COVID-19 animal model: A better therapeutic outcome of gold cluster.

He, Z., Ye, F., Zhang, C., Fan, J., Du, Z., Zhao, W., Yuan, Q., Niu, W., Gao, F., He, B., Cao, P., Zhao, L., Gao, X., Gao, X., Sun, B., Dong, Y., Zhao, J., Qi, J., Liang, X.J., Jiang, H., Gong, Y., Tan, W., Gao, X.

(2022) Nano Today 44: 101468

DOI: https://doi.org/10.1016/j.nantod.2022.101468

Macromolecule Content

Total Structure Weight: 34.22 kDa
Atom Count: 2,441
Modeled Residue Count: 301
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COVID-19 MAIN PROTEASE	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (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
AU (Subject of Investigation/LOI) Query on AU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.194 (Depositor), 0.195 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.279	α = 90
b = 53.985	β = 101.849
c = 44.678	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-11-03
Type: Initial release
Version 1.1: 2022-04-27
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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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.