8BSD

SARS-CoV-2 nsp10-16 methyltransferase in complex with tubercidin

PDB DOI: https://doi.org/10.2210/pdb8BSD/pdb

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

Deposited: 2022-11-24 Released: 2022-12-07
Deposition Author(s): Kremling, V., Oberthuer, D., Sprenger, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.207
R-Value Work: 0.180
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 1.1 of the entry. See complete history.

Literature

Crystal structures of Tubercidin bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16

Kremling, V., Oberthuer, D., Sprenger, J.

To be published.

Macromolecule Content

Total Structure Weight: 51.6 kDa
Atom Count: 3,786
Modelled Residue Count: 417
Deposited Residue Count: 444
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	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% 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
TBN (Subject of Investigation/LOI) Query on TBN Download Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL C₁₁ H₁₄ N₄ O₄ HDZZVAMISRMYHH-KCGFPETGSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B]	HA [auth B], IA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] C [auth A] CA [auth A] D [auth A] AA [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], F [auth A], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A]	EA [auth A], FA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A]