6XKM

Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with SAM Determined by Fixed-Target Serial Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report



Literature

Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with SAM Determined by Fixed-Target Serial Crystallography

Wilamowski, M.Sherrell, D.A.Minasov, G.Kim, Y.Shuvalova, L.Lavens, A.Chard, R.Rosas-Lemus, M.Maltseva, N.Jedrzejczak, R.Michalska, K.Satchell, K.J.F.Joachimiak, A.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2'-O-methyltransferaseA301Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 2.1.1 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 10B142Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.41α = 90
b = 170.41β = 90
c = 52.631γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
DIALSdata scaling
DIALSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 2.0: 2020-08-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary