Structure of IDP52015

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with potential repurposing drug Tipiracil

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CSGID target
IDP52015 
PDB Id
6WXC (NCBI MMDB) 
Authors
Kim, Y., Maltseva, N., Jedrzejczak, R., Endres, M., Godzik, A., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases  
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
May 10, 2020 
Release Date
May 20, 2020 

Annotation

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Ligands

Ligand code Name Ligand type
LIG 3-pyridin-4-yl-2,4-dihydro-indeno[1,2-.c.]pyrazole biological
PO4 crystallization
EDO ethylene diol crystallization
FMT formate crystallization

Structure information

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Unit cell parameters

Space Group
P 63  
Unit Cell

a=150.86Å, b=150.86Å, c=111.70Å
α=90.00, β=90.00, γ=120.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
42.45-1.85Å (1.87-1.85Å)  
Rall(%)
17.2 
Rwork(%)
17.1 (34.2) 
Rfree(%)
19.4 (33.4) 
Num. observed reflections
127822 (3244) 
Num. Rfree reflections
6301 (147) 
Completeness(%)
99.1 (79.0) 

Model parameters

Num Atoms
5647  
Num Waters
702  
Num Hetatoms
792  
Model mean isotropic B factor
41.140Å2  
RMSD bond length
0.015Å  
RMSD bond angle
1.251°  
RMSD dihedral angle
20.19°
 
Filename uploaded
NSP15-Tipi_185.pdb (uploaded on Jul 28, 2020 6:32 PM)  
Inserted
Jul 28, 2020