5WFI | pdb_00005wfi

X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb5WFI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Murine hepatitis virus strain A59, Homo sapiens
• Expression System: Escherichia coli, Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2017-07-12 Released: 2018-08-01 
• Deposition Author(s): Mesecar, A.D., Chen, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin

Mesecar, A.D., Chen, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.08 kDa 
• Atom Count: 6,696 
• Modelled Residue Count: 756 
• Deposited Residue Count: 758 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
papain-like protease	A, B	303	Murine hepatitis virus strain A59	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22
UniProt
Find proteins for P0C6X9 (Murine coronavirus (strain A59)) Explore P0C6X9  Go to UniProtKB:  P0C6X9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, D	76	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth D], R [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	I [auth A], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	H [auth A], M [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.515	α = 90
b = 43.388	β = 114.85
c = 110.159	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Mesecar, A.D., Chen, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI085089

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary