7I1F | pdb_00007i1f

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G04 from the F2X-Entry Screen in orthorhombic space group

PDB DOI: https://doi.org/10.2210/pdb7I1F/pdb
Deposition Group: G_1002335 (changed state) | Explore G_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: 1.77 Å
R-Value Free:
0.260 (Depositor), 0.262 (DCC)
R-Value Work:
0.217 (Depositor), 0.225 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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: 68.11 kDa
Atom Count: 5,000
Modeled Residue Count: 602
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T9V (Subject of Investigation/LOI) Query on T9V 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]	N-(4-methoxyphenyl)acetamide C₉ H₁₁ N O₂ XVAIDCNLVLTVFM-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	D [auth A], G [auth B], H [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.260 (Depositor), 0.262 (DCC)
R-Value Work: 0.217 (Depositor), 0.225 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.69	α = 90
b = 99.33	β = 90
c = 103.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
European Commission	European Union	871037

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release
Version 2.0: 2026-03-18
Type: Coordinate replacement
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary

7I1F | pdb_00007i1f

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G04 from the F2X-Entry Screen in orthorhombic space group

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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