7MC9

X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA

PDB DOI: https://doi.org/10.2210/pdb7MC9/pdb

Classification: HYDROLASE
Organism(s): Porcine epidemic diarrhea virus, Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Escherichia coli
Mutation(s): No

Deposited: 2021-04-01 Released: 2021-07-07
Deposition Author(s): Durie, I.A., Dzimianski, J.V., Daczkowski, C.M., Pegan, S.D.
Funding Organization(s): United States Department of Agriculture (USDA), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.257
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin

Durie, I.A., Dzimianski, J.V., Daczkowski, C.M., McGuire, J., Faaberg, K., Pegan, S.D.

(2021) Acta Cryst D 77: 943-953

DOI: https://doi.org/10.1107/S205979832100509X

Macromolecule Content

Total Structure Weight: 276.03 kDa
Atom Count: 19,153
Modelled Residue Count: 2,465
Deposited Residue Count: 2,496
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, C, E, G, I A, C, E, G, I, K, M, O	237	Porcine epidemic diarrhea virus	Mutation(s): 0 Gene Names: ORF1ab EC: 3.4.19.12 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for A0A059VJE6 (Porcine epidemic diarrhea virus) Explore A0A059VJE6 Go to UniProtKB: A0A059VJE6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A059VJE6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, D, F, H, J B, D, F, H, J, L, N, P	75	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain DA [auth I] SDF format, chain FA [auth K] SDF format, chain HA [auth M] SDF format, chain IA [auth M] SDF format, chain KA [auth O] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth C] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth M] MOL2 format, chain IA [auth M] MOL2 format, chain KA [auth O] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth C] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	AA [auth G] BA [auth G] DA [auth I] FA [auth K] HA [auth M] AA [auth G], BA [auth G], DA [auth I], FA [auth K], HA [auth M], IA [auth M], KA [auth O], Q [auth A], R [auth A], S [auth A], U [auth C], W [auth E], X [auth E], Y [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth I] Focus chain FA [auth K] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain KA [auth O] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth C] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth I] Focus chain FA [auth K] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain KA [auth O] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth C] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E]
AYE Query on AYE Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain EA [auth J] SDF format, chain GA [auth L] SDF format, chain JA [auth N] SDF format, chain LA [auth P] SDF format, chain T [auth B] SDF format, chain V [auth D] SDF format, chain Z [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain EA [auth J] MOL2 format, chain GA [auth L] MOL2 format, chain JA [auth N] MOL2 format, chain LA [auth P] MOL2 format, chain T [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth F]	CA [auth H] EA [auth J] GA [auth L] JA [auth N] LA [auth P] CA [auth H], EA [auth J], GA [auth L], JA [auth N], LA [auth P], T [auth B], V [auth D], Z [auth F]	prop-2-en-1-amine C₃ H₇ N VVJKKWFAADXIJK-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain EA [auth J] Focus chain GA [auth L] Focus chain JA [auth N] Focus chain LA [auth P] Focus chain T [auth B] Focus chain V [auth D] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth H] Focus chain EA [auth J] Focus chain GA [auth L] Focus chain JA [auth N] Focus chain LA [auth P] Focus chain T [auth B] Focus chain V [auth D] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.257
R-Value Work: 0.200
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.138	α = 90
b = 136.873	β = 90
c = 193.348	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Funding Organization	Location	Grant Number
United States Department of Agriculture (USDA)	United States	58-5030-5034
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI151006
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI109008

Revision History (Full details and data files)

Version 1.0: 2021-07-07
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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Help and Resources

7MC9

X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA

Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources