1DLK

CRYSTAL STRUCTURE ANALYSIS OF DELTA-CHYMOTRYPSIN BOUND TO A PEPTIDYL CHLOROMETHYL KETONE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of delta-chymotrypsin bound to a peptidyl chloromethyl ketone inhibitor.

Mac Sweeney, A.Birrane, G.Walsh, M.A.O'Connell, T.Malthouse, J.P.Higgins, T.M.

(2000) Acta Crystallogr.,Sect.D 56: 280-286


  • PubMed Abstract: 
  • Chymotrypsin is a member of the trypsin family of serine proteases and is one of the first proteins successfully studied by X-ray crystallography. It is secreted into the intestine as the inactive precursor chymotrypsinogen; four sequential cleavages ...

    Chymotrypsin is a member of the trypsin family of serine proteases and is one of the first proteins successfully studied by X-ray crystallography. It is secreted into the intestine as the inactive precursor chymotrypsinogen; four sequential cleavages of the peptide bonds following residues 13, 15, 146 and 148 occur to generate the active pi, delta, kappa and alpha forms of chymotrypsin. (13)C NMR has shown [O'Connell & Malthouse (1995). Biochem. J. 307, 353-359] that when the delta form of chymotrypsin is inhibited by 2-(13)C-enriched benzyloxycarbonylglycylglycylphenylalanyl chloromethane, a tetrahedral adduct is formed which is thought to be analogous to the tetrahedral intermediate formed during catalysis. This inhibitor complex has been crystallized as a dimer in space group P4(1)2(1)2. The structure has been refined at 2.14 A resolution to an R value of 21.2% (free R = 25.2%). Conformational differences between delta-chymotrypsin and chymotrypsinogen in the region of the flexible autolysis loop (residues 145-150) were observed. This is the first crystal structure of delta-chymotrypsin and includes two residues which are disordered in previous crystal structures of active chymotrypsin. A difference of 11.3 A(2) between the average B values of the monomers within the asymmetric unit is caused by lattice-disordering effects approximating to rotation of the molecules about a crystallographic screw axis. The substrate-binding mode of the inhibitor was similar to other chymotrypsin peptidyl inhibitor complexes, but this is the first published chymotrypsin structure in which the tetrahedral chloromethyl ketone transition-state analogue is observed. This structure is compared with that of a similar tetrahedral transition-state analogue which does not alkylate the active-site histidine residue.


    Organizational Affiliation

    Department of Chemistry, NUI Galway, Galway, Ireland. macsweeney@biocfebs.unizh.ch




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
A, C
13Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
B, D
230Bos taurusMutation(s): 0 
EC: 3.4.21.1
Find proteins for P00766 (Bos taurus)
Go to UniProtKB:  P00766
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptidic inhibitor
E, F
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001053 (Y3A)
Query on PRD_001053
EZ-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM)Peptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.170α = 90.00
b = 121.170β = 90.00
c = 116.080γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2018-09-12
    Type: Advisory, Data collection, Structure summary