8G62

Papain-Like Protease of SARS CoV-2 in complex with remodilin NCGC 390004


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3
A, B, C
318Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data)
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YOO
Query on YOO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
M [auth A]
O [auth B]
U [auth C]
E [auth A],
F [auth A],
M [auth A],
O [auth B],
U [auth C],
W [auth C]
3-methoxy-5-(1-methylpiperidin-4-yl)-N-[4-(pyrrolidine-1-sulfonyl)phenyl]benzamide
C24 H31 N3 O4 S
JTGUXSIYSIXMPK-UHFFFAOYSA-N
ZN
Query on ZN

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D [auth A],
N [auth B],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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J [auth A]
K [auth A]
L [auth A]
S [auth B]
T [auth B]
J [auth A],
K [auth A],
L [auth A],
S [auth B],
T [auth B],
Z [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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H [auth A]
I [auth A]
Q [auth B]
R [auth B]
X [auth C]
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
X [auth C],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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G [auth A],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.02α = 90
b = 170.02β = 90
c = 97.588γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


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 States75N93022C00035

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection