9EMV

SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA (Cap0-analog)/m7GpppAm (Cap1-analog)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2'-O-methyltransferase nsp16304Severe 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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V9G (Subject of Investigation/LOI)
Query on V9G

Download Ideal Coordinates CCD File 
M [auth A]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE
C22 H32 N10 O17 P3
WZAAWBDISKLAIE-NAGRZYTCSA-N
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
SAH
Query on SAH

Download Ideal Coordinates CCD File 
F [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SGV (Subject of Investigation/LOI)
Query on SGV

Download Ideal Coordinates CCD File 
C [auth A]SANGIVAMYCIN
C12 H15 N5 O5
OBZJZDHRXBKKTJ-JTFADIMSSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.51α = 90
b = 169.51β = 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
Not fundedGermanyDESY Strategy Fund MUXCOSDYN

Revision History  (Full details and data files)

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