8VUO | pdb_00008vuo

Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA

PDB DOI: https://doi.org/10.2210/pdb8VUO/pdb
NAKB: 8VUO

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

Deposited: 2024-01-29 Released: 2025-02-05
Deposition Author(s): Misra, A., Rahisuddin, R., Gupta, Y.K.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.219 (Depositor), 0.221 (DCC)
R-Value Work:
0.180 (Depositor), 0.187 (DCC)
R-Value Observed:
0.182 (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 SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA

Misra, A., Rahisuddin, R., Gupta, Y.K.

To be published.

Macromolecule Content

Total Structure Weight: 105.71 kDa
Atom Count: 7,218
Modelled Residue Count: 846
Deposited Residue Count: 894
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A, C	298	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B, D	139	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

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(APUPUPAPAPAPGPGPUPU)-3')	E, F	10	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
M7G Query on M7G Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain FA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth F]	EA [auth E], FA [auth F]	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE C₁₁ H₁₈ N₅ O₁₁ P₂ SBASPRRECYVBRF-KQYNXXCUSA-O		Interactions Focus chain EA [auth E] Focus chain FA [auth F] Interactions & Density Focus chain EA [auth E] Focus chain FA [auth F]
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain H [auth A] MOL2 format, chain U [auth C] MOL2 format, chain H [auth A] mmCIF format, chain U [auth C] mmCIF format, chain H [auth A]	H [auth A], U [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain H [auth A] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain U [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	BA [auth D], CA [auth D], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] 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 V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] 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 V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] 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 V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] DA [auth D] I [auth A] J [auth A] K [auth A] AA [auth C], DA [auth D], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain DA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth C] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C]	G [auth A], T [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain T [auth C]