1PQ8

Trypsin at pH 4 at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Work: 0.128 

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:  
    1PQ8, 1PQ7, 1PQ5, 1PQA, 1PPZ

  • 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 multipole refinement ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TrypsinA224Fusarium oxysporumMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P35049 (Fusarium oxysporum)
Explore P35049 
Go to UniProtKB:  P35049
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GLY-GLY-ARG PEPTIDEB [auth C]3N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
G [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

Download Ideal Coordinates CCD File 
F [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Work: 0.128 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.93α = 102.67
b = 36.887β = 104.66
c = 39.744γ = 102.61
Software Package:
Software NamePurpose
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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