8S8W | pdb_00008s8w

SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA-RNA (Cap0-RNA)

PDB DOI: https://doi.org/10.2210/pdb8S8W/pdb
NAKB: 8S8W

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

Deposited: 2024-03-07 Released: 2024-03-20
Deposition Author(s): Kremling, V., Sprenger, J., Oberthuer, D., Scheer, T.E.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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 discovery

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

(2024) Elife

DOI: https://doi.org/10.7554/elife.98310.1

Macromolecule Content

Total Structure Weight: 51.91 kDa
Atom Count: 3,591
Modeled Residue Count: 416
Deposited Residue Count: 447
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase nsp16	A	304	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
m7GpppA-RNA (Cap0-RNA)	C	3	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C₂₁ H₃₀ N₁₀ O₁₇ P₃ QQOHNVHGNZYSBP-XPWFQUROSA-O		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
SAM Query on SAM 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]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SGV (Subject of Investigation/LOI) Query on SGV Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SANGIVAMYCIN C₁₂ H₁₅ N₅ O₅ OBZJZDHRXBKKTJ-JTFADIMSSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]