5S4D

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z1741982441


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report




Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 3AB169Severe 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
2OP
Query on 2OP

Download Ideal Coordinates CCD File 
A
(2S)-2-HYDROXYPROPANOIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-REOHCLBHSA-N
 Ligand Interaction
LAC
Query on LAC

Download Ideal Coordinates CCD File 
A
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.313α = 90
b = 88.313β = 90
c = 39.19γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release