1PQ7

Trypsin at 0.8 A, pH5 / borax


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Work: 0.109 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Trypsin Revisited: CRYSTALLOGRAPHY AT (SUB) ATOMIC RESOLUTION AND QUANTUM CHEMISTRY REVEALING DETAILS OF CATALYSIS.

Schmidt, A.Jelsch, C.Ostergaard, P.Rypniewski, W.Lamzin, V.S.

(2003) J.Biol.Chem. 278: 43357-43362

  • DOI: 10.1074/jbc.M306944200
  • Primary Citation of Related Structures:  1PPZ, 1PQ5, 1PQ8, 1PQA

  • PubMed Abstract: 
  • A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and ...

    A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL) Hamburg c/o DESY, D-22607 Hamburg, Germany. andrea@embl-hamburg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin
A
224Fusarium oxysporumEC: 3.4.21.4
Find proteins for P35049 (Fusarium oxysporum)
Go to UniProtKB:  P35049
Small Molecules
Ligands 2 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
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.8 Å
  • R-Value Work: 0.109 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 32.869α = 102.89
b = 37.022β = 104.59
c = 39.780γ = 102.37
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description