5YNP

Crystal structure of MERS-CoV nsp16/nsp10 complex bound to sinefungin and m7GpppA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex

Wei, S.M.Yang, L.Ke, Z.H.Liu, Q.Y.Yang, Z.Z.Chen, Y.Guo, D.Y.Fan, C.P.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
nsp16 protein
A
303Human betacoronavirus 2c EMC/2012Mutation(s): 0 
Gene Names: orf1ab
Find proteins for K0BWD0 (Human betacoronavirus 2c EMC/2012)
Go to UniProtKB:  K0BWD0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nsp10 protein
B
140Human betacoronavirus 2c EMC/2012Mutation(s): 0 
Gene Names: orf1ab
Find proteins for K4LC41 (Human betacoronavirus 2c EMC/2012)
Go to UniProtKB:  K4LC41
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
SINEFUNGIN
ADENOSYL-ORNITHINE
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
GTA
Query on GTA

Download SDF File 
Download CCD File 
A
P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
7-METHYL-GPPPA
C21 H30 N10 O17 P3
QQOHNVHGNZYSBP-XPWFQUROSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.880α = 90.00
b = 70.045β = 90.00
c = 119.720γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NSFCChina31570762

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release