1FNI

CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.01% POLYDOCANOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of porcine beta-trypsin-detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol.

Deepthi, S.Johnson, A.Pattabhi, V.

(2001) Acta Crystallogr.,Sect.D 57: 1506-1512

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polydocanol has a wide range of medical applications, especially in sclerotherapy of many diseases such as gastrointestinal antiplastia, oesophageal haemangioma etc. It is of interest to study the mode of binding of this medically important detergent ...

    Polydocanol has a wide range of medical applications, especially in sclerotherapy of many diseases such as gastrointestinal antiplastia, oesophageal haemangioma etc. It is of interest to study the mode of binding of this medically important detergent and its subsequent action on proteins. Here, three crystal structures of serine protease trypsin are reported in the presence of varying concentrations of polydocanol in order to elucidate its mode of binding and interactions with proteins. Polydocanol binds to the protein with its hydrophilic head rather than the hydrophobic tail as is the case with other detergents such as SDS and MEGA-8. This hydrophilic binding mode results in the binding sites of polydocanol being distributed on the surface of the enzyme. There are at least 11 binding sites for polydocanol in trypsin. Polydocanol forms part of the large-scale water networks which connect distant regions of the enzyme, thereby stabilizing it. The hydrophilic binding of polydocanol also results in cross-linked pairs of trypsin molecules.


    Related Citations: 
    • Crystal Structure at 1.63 Angstroms Resolution of the Native Form of Porcine Beta Trypsin : Revealing an Acetate Ion Binding Site and Functional Water Network
      Johnson, A.,Gautham, N.,Pattabhi, V.
      (1999) BIOCHIM.BIOPHYS.ACTA 1435: 7
    • The First Structure at 1.8 Angstroms Resolution of an Active Autolysate Form of Porcine Alpha Trypsin
      Johnson, A.,Krishnaswamy, S.,Sundaram, P.V.,Pattabhi, V.
      (1997) Acta Crystallogr.,Sect.D 53: 311


    Organizational Affiliation

    Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPSIN
A
223Sus scrofaMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00761 (Sus scrofa)
Go to UniProtKB:  P00761
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.804α = 90.00
b = 53.946β = 90.00
c = 47.201γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AUTOMARdata reduction
XDSdata reduction
X-PLORphasing
X-PLORmodel building
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-04-04
    Type: Data collection