4QRV | pdb_00004qrv

Crystal structure of I86F mutant of papain

• PDB DOI: https://doi.org/10.2210/pdb4QRV/pdb

• Classification: HYDROLASE
• Organism(s): Carica papaya
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-07-02 Released: 2015-08-12 
• Deposition Author(s): Dutta, S., Choudhury, D., Roy, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Pro-peptide regulates the substrate specificity and zymogen activation process of papain: A structural and mechanistic insight

Dutta, S., Choudhury, D., Roy, S., Biswas, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 82.32 kDa 
• Atom Count: 5,191 
• Modeled Residue Count: 603 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain	A, B	363	Carica papaya	Mutation(s): 5  EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya) Explore P00784  Go to UniProtKB:  P00784

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.67	α = 90
b = 74.267	β = 92.85
c = 116.326	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Dutta, S., Choudhury, D., Roy, S.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary