Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.90 kDa 
• Atom Count: 6074 
• Residue Count: 698 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

6X1B

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.

• DOI: 10.2210/pdb6X1B/pdb
• NDB: 6X1B

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-18 Released: 2020-05-27 
• Deposition Author(s): Kim, Y., Maltseva, N., Jedrzejczak, R., Welk, L., Endres, M., Chang, C., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.165 

Literature

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Kim, Y., Wower, J., Maltseva, N., Chang, C., Jedrzejczak, R., Wilamowski, M., Kang, S., Nicolaescu,, N., Randall, G., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

(2020) Biorxiv 

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease	A, B	370	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-R(*GP*U)-3')	D, F	2	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.165 
• Space Group: P 6₃
• Diffraction Data DOI: 10.18430/m36x1b Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.875	α = 90
b = 150.875	β = 90
c = 111.73	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-05-18 
• Released Date: 2020-05-27 
Deposition Author(s): Kim, Y., Maltseva, N., Jedrzejczak, R., Welk, L., Endres, M., Chang, C., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History 

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 2.0: 2020-06-10
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-08-05
  Changes: Database references, Structure summary
• Version 2.2: 2020-12-09
  Changes: Database references