7MC9 | pdb_00007mc9

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 (Depositor), 0.256 (DCC)
R-Value Work:
0.200 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 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
Modeled Residue Count: 2,465
Deposited Residue Count: 2,496
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A059VJE6
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain U [auth C] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain KA [auth O] SDF format, chain IA [auth M] SDF format, chain HA [auth M] SDF format, chain FA [auth K] SDF format, chain DA [auth I] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain U [auth C] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain KA [auth O] MOL2 format, chain IA [auth M] MOL2 format, chain HA [auth M] MOL2 format, chain FA [auth K] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain U [auth C] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain KA [auth O] mmCIF format, chain IA [auth M] mmCIF format, chain HA [auth M] mmCIF format, chain FA [auth K] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	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 G] SDF format, chain EA [auth I] SDF format, chain GA [auth K] SDF format, chain JA [auth M] SDF format, chain T [auth A] SDF format, chain V [auth C] SDF format, chain Z [auth E] SDF format, chain LA [auth O] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth K] MOL2 format, chain JA [auth M] MOL2 format, chain T [auth A] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth E] MOL2 format, chain LA [auth O] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth K] mmCIF format, chain JA [auth M] mmCIF format, chain T [auth A] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth E] mmCIF format, chain LA [auth O]	CA [auth G] EA [auth I] GA [auth K] JA [auth M] LA [auth O] CA [auth G], EA [auth I], GA [auth K], JA [auth M], LA [auth O], T [auth A], V [auth C], Z [auth E]	prop-2-en-1-amine C₃ H₇ N VVJKKWFAADXIJK-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth I] Focus chain GA [auth K] Focus chain JA [auth M] Focus chain LA [auth O] Focus chain T [auth A] Focus chain V [auth C] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth I] Focus chain GA [auth K] Focus chain JA [auth M] Focus chain LA [auth O] Focus chain T [auth A] Focus chain V [auth C] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.257 (Depositor), 0.256 (DCC)
R-Value Work: 0.200 (Depositor), 0.201 (DCC)
R-Value Observed: 0.203 (Depositor)

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

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View more in-depth experimental data

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
Version 2.0: 2024-12-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary