8G62

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

PDB DOI: https://doi.org/10.2210/pdb8G62/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-02-14 Released: 2023-02-22
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Jedrzejczak, R., Luci, D., Kales, S., Simeonov, A., Rai, G., Drayman, N., Tay, S., Oakes, S., Rosner, M., Chen, B., Dulin, N., Solway, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.214 (Depositor), 0.210 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Osipiuk, J., Tesar, C., Endres, M., Jedrzejczak, R., Luci, D., Kales, S., Simeonov, A., Rai, G., Drayman, N., Tay, S., Oakes, S., Rosner, M., Chen, B., Dulin, N., Solway, J., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 111.39 kDa
Atom Count: 8,110
Modelled Residue Count: 941
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A, B, C	318	Severe acute respiratory syndrome coronavirus 2	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YOO Query on YOO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain W [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain W [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain W [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	D [auth A], N [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain V [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	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		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.214 (Depositor), 0.210 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Diffraction Data: https://doi.org/10.18430/m38g62

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.02	α = 90
b = 170.02	β = 90
c = 97.588	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035