9GTF

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256190


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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 structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders

Kremling, V.Sprenger, J.Oberthuer, D.Chapman, H.N.Middendorf, P.Falke, S.Kiene, A.Klopprogge, B.Scheer, T.E.S.Creon, A.

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
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  • 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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IOV
Query on A1IOV

Download Ideal Coordinates CCD File 
N [auth A]7-[(3~{R},4~{R},6~{S})-1-[(2~{S})-2-azanyl-4-methyl-pentanoyl]-4-methyl-4,6-bis(oxidanyl)azepan-3-yl]-1,3-dimethyl-purine-2,6-dione
C20 H32 N6 O5
FFMPXKQMGDIWEU-LKWXMQFFSA-N
SAM
Query on SAM

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M [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
MES
Query on MES

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D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN
Query on ZN

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P [auth B],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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C [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
C [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
R [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
T [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.33α = 90
b = 169.33β = 90
c = 51.87γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
Cootmodel building
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedDESY Strategy Fund MUXCOSDYN

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release