7THH

SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Papain-like protease nsp3
A, B, C, D, E, F
A, B, C, D, E, F
131Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
O [auth C]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
K [auth B],
M [auth C],
N [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
R [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth A],
P [auth E],
Q [auth E],
S [auth F],
G [auth A],
J [auth A],
P [auth E],
Q [auth E],
S [auth F],
T [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.173α = 90
b = 113.693β = 93.02
c = 109.688γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release