5XW1 | pdb_00005xw1

Crystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, PRN, at pH10

• PDB DOI: https://doi.org/10.2210/pdb5XW1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa, Capsicum annuum
• Mutation(s): No 


• Deposited: 2017-06-28 Released: 2018-07-04 
• Deposition Author(s): Saikhedkar, N.S., Bhoite, A.S., Giri, A.P., Kulkarni, K.A.
• Funding Organization(s): CSIR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Reactive centre loop peptides devoid of potato protease inhibitor-II protein scaffold inhibit serine proteases

Joshi, R.S., Saikhedkar, N.S., Bhoite, A.S., Mohandasan, R., Yadav, A.K., Fernandes, M., Kulkarni, K.A., Giri, A.P.

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)

Macromolecule Content 

• Total Structure Weight: 25.25 kDa 
• Atom Count: 1,910 
• Modeled Residue Count: 226 
• Deposited Residue Count: 235 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	A	133	Sus scrofa	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761  Go to UniProtKB:  P00761

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	B	98	Sus scrofa	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761  Go to UniProtKB:  P00761

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylated-Pro-Arg-Asn Inhibitor	C	4	Capsicum annuum	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth B], F [auth B], G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.165	α = 90
b = 83.165	β = 90
c = 135.232	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Saikhedkar, N.S., Bhoite, A.S., Giri, A.P., Kulkarni, K.A.

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Funding Organization	Location	Grant Number
CSIR	India	BSC0120

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary