1PQ8

Trypsin at pH 4 at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 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:  

  • 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 oxysporumMutation(s): 0 
EC: 3.4.21.4
Find proteins for P35049 (Fusarium oxysporum)
Go to UniProtKB:  P35049
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLY-GLY-ARG PEPTIDE
C
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Work: 0.128 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 32.930α = 102.67
b = 36.887β = 104.66
c = 39.744γ = 102.61
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
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