9P6P | pdb_00009p6p

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).

PDB DOI: https://doi.org/10.2210/pdb9P6P/pdb
NAKB: 9P6P

Classification: TRANSFERASE, Viral Protein
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-19 Released: 2025-07-02
Deposition Author(s): Minasov, G., Shuvalova, L., Maltseva, N., Kim, Y., Kiryukhina, O., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.193 (Depositor), 0.198 (DCC)
R-Value Work:
0.168 (Depositor), 0.174 (DCC)
R-Value Observed:
0.169 (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

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).

Minasov, G., Shuvalova, L., Maltseva, N., Kim, Y., Kiryukhina, O., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 103.86 kDa
Atom Count: 7,613
Modeled Residue Count: 848
Deposited Residue Count: 894
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	A, C	301	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.1.1
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, D	142	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
RNA (5'-D((M7G))-R(PAPUPU)-3')	E, F [auth G]	4	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGT Query on MGT Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C₁₁ H₂₀ N₅ O₁₄ P₃ BUJQMJUTTBGELS-KQYNXXCUSA-N		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain G [auth A] MOL2 format, chain X [auth C] MOL2 format, chain G [auth A] mmCIF format, chain X [auth C] mmCIF format, chain G [auth A]	G [auth A], X [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain G [auth A] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain X [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	EA [auth C] FA [auth C] GA [auth C] HA [auth C] IA [auth C] EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], S [auth A], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain MA [auth D] SDF format, chain LA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain LA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain LA [auth D]	LA [auth D], MA [auth D], T [auth B], U [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain LA [auth D] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] H [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], NA [auth D], OA [auth D], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain Z [auth C]