3VPK

Crystal Structure of 6-Guanidinohexanoyl Trypsin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated

Masuda, Y.Nitanai, Y.Mizutani, R.Noguchi, S.

(2012) Proteins --: --

  • DOI: 10.1002/prot.24206

  • PubMed Abstract: 
  • The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optim ...

    The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optimum reaction pH, at 1.94 Å resolution. In this structure, three water molecules are observed around the catalytic site. One acts as a nucleophile to attack the acyl carbonyl carbon while the other two waters fix the position of the catalytic water through a hydrogen bond. When the acyl carbonyl oxygen oscillates thermally, the water assumes an appropriate angle to catalyze the deacylation.


    Organizational Affiliation

    Nuclear, Biological and Chemical Detection Technology Section, Human Oriented Systems Division, Advanced Defense Technology Center, Technical Research and Development Institute, Ministry of Defense, Meguro, Tokyo 153-8630, Japan. mas@cs.trdi.mod.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E4B
Query on E4B

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A
ethyl 4-hydroxybenzoate
Ethyl p-hydroxybenzoate
C9 H10 O3
NUVBSKCKDOMJSU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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Download CCD File 
A
6-carbamimidamidohexanoic acid
C7 H15 N3 O2
NSDYIDKTTPXCRH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.779α = 90.00
b = 61.050β = 90.00
c = 69.664γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-02-06
    Type: Database references