9GUY | pdb_00009guy

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571098

PDB DOI: https://doi.org/10.2210/pdb9GUY/pdb

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

Deposited: 2024-09-20 Released: 2024-12-04
Deposition Author(s): Kremling, V., Sprenger, J., Oberthuer, D., Kiene, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.213 (Depositor), 0.212 (DCC)
R-Value Work:
0.184 (Depositor), 0.193 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders

Kremling, V., Sprenger, J., Oberthuer, D., Chapman, H.N., Middendorf, P., Falke, S., Kiene, A., Klopprogge, B., Scheer, T.E.S., Creon, A.

To be published.

Macromolecule Content

Total Structure Weight: 51.76 kDa
Atom Count: 3,760
Modeled Residue Count: 416
Deposited Residue Count: 444
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase nsp16	A [auth B]	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 [auth C]	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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IOL (Subject of Investigation/LOI) Query on A1IOL Download:Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	~{N}-[(5~{S})-5-azanyl-6-[(3~{S},4~{S},6~{R})-3-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]-4-methyl-4,6-bis(oxidanyl)azepan-1-yl]-6-oxidanylidene-hexyl]ethanamide C₂₂ H₃₅ N₇ O₆ GVNVRCRSNWOHEA-YDGQEPMXSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C]	CA [auth C], DA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain C [auth B] SDF format, chain E [auth B] SDF format, chain EA [auth C] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain GA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth B] MOL2 format, chain E [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain GA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth B] mmCIF format, chain E [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain GA [auth C]	AA [auth B] BA [auth B] C [auth B] E [auth B] EA [auth C] AA [auth B], BA [auth B], C [auth B], E [auth B], EA [auth C], F [auth B], G [auth B], GA [auth C], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth B] Focus chain E [auth B] Focus chain EA [auth C] Focus chain F [auth B] Focus chain G [auth B] Focus chain GA [auth C] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth B] Focus chain E [auth B] Focus chain EA [auth C] Focus chain F [auth B] Focus chain G [auth B] Focus chain GA [auth C] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain FA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain FA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain FA [auth C]	FA [auth C], W [auth B], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth C] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain FA [auth C] Focus chain W [auth B] Focus chain X [auth B]