3S8J

Crystal structure of a papaya latex serine protease inhibitor (PPI) at 2.6A resolution

• PDB DOI: https://doi.org/10.2210/pdb3S8J/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Carica papaya
• Mutation(s): No 


• Deposited: 2011-05-29 Released: 2011-11-02 
• Deposition Author(s): Garcia-Pino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.213 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 

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: 42.29 kDa 
• Atom Count: 2,911 
• Modelled Residue Count: 363 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Latex serine proteinase inhibitor	A, B	184	Carica papaya	Mutation(s): 0
UniProt
Find proteins for P80691 (Carica papaya) Explore P80691  Go to UniProtKB:  P80691

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	F [auth A], L [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.213 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.699	α = 90
b = 74.699	β = 90
c = 78.97	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Garcia-Pino, A.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary