7I15 | pdb_00007i15

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment C02 from the F2X-Entry Screen in orthorhombic space group

PDB DOI: https://doi.org/10.2210/pdb7I15/pdb
Deposition Group: G_1002335 (changed state) ExploreG_1002335

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

Deposited: 2025-02-03 Released: 2025-05-21
Deposition Author(s): Barthel, T., Benz, L.S., Wollenhaupt, J., Weiss, M.S.
Funding Organization(s): European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.282 (Depositor), 0.283 (DCC)
R-Value Work:
0.239 (Depositor), 0.243 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening

Barthel, T., Wollenhaupt, J., Benz, L.S., Reincke, P., Zhang, L., Lennartz, F., Tabermann, H., Mueller, U., Meente, A., Hilgenfeld, R., Weiss, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 68.24 kDa
Atom Count: 5,726
Modeled Residue Count: 602
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SYA (Subject of Investigation/LOI) Query on SYA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	2,4,5-tris(fluoranyl)-3-methoxy-benzoic acid C₈ H₅ F₃ O₃ YVJHZWWMKFQKDC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]