9EMJ

SARS-CoV-2 methyltransferase nsp10-16 in complex with Toyocamycin and m7GpppA (Cap0-analog)

PDB DOI: https://doi.org/10.2210/pdb9EMJ/pdb

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

Deposited: 2024-03-08 Released: 2024-03-20
Deposition Author(s): Kremling, V., Sprenger, J., Oberthuer, D., Kiene, A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.207
R-Value Work: 0.181
R-Value Observed: 0.181

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

SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug development

Kremling, V., Sprenger, J., Oberthuer, D., Chapman, H.N., Middendorf, P., Fernandez-Garcia, Y., Ehrt, C., Falke, S., Kiene, A., Klopprogge, B., Scheer, T.E.S., Rarey, M., Barthels, F., Kuehn, S., Guenther, S.

To be published.

Macromolecule Content

Total Structure Weight: 50.64 kDa
Atom Count: 3,762
Modelled Residue Count: 416
Deposited Residue Count: 443
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase nsp16	A	303	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.1.1.57
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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B	140	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTA (Subject of Investigation/LOI) Query on GTA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C₂₁ H₃₀ N₁₀ O₁₇ P₃ QQOHNVHGNZYSBP-XPWFQUROSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MGP Query on MGP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE C₁₁ H₁₉ N₅ O₁₄ P₃ DKVRNHPCAOHRSI-KQYNXXCUSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
TO1 (Subject of Investigation/LOI) Query on TO1 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]	4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile C₁₂ H₁₃ N₅ O₄ XOKJUSAYZUAMGJ-WOUKDFQISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth B] mmCIF format, chain I [auth B]	F [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth B] Interactions & Density Focus chain F [auth B] Focus chain I [auth B]