9EMJ

SARS-CoV-2 methyltransferase nsp10-16 in complex with Toyocamycin and m7GpppA (Cap0-analog)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • 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 1.0 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 development

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2'-O-methyltransferase nsp16303Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 10140Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTA (Subject of Investigation/LOI)
Query on GTA

Download Ideal Coordinates CCD File 
D [auth A]P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
C21 H30 N10 O17 P3
QQOHNVHGNZYSBP-XPWFQUROSA-O
MGP
Query on MGP

Download Ideal Coordinates CCD File 
E [auth A]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
TO1 (Subject of Investigation/LOI)
Query on TO1

Download Ideal Coordinates CCD File 
C [auth A]4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
C12 H13 N5 O4
XOKJUSAYZUAMGJ-WOUKDFQISA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.7α = 90
b = 168.7β = 90
c = 52.25γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentDESY Strategy Fund MUXCOSDYN

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release