1CZI

CHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A 2.3 A resolution structure of chymosin complexed with a reduced bond inhibitor shows that the active site beta-hairpin flap is rearranged when compared with the native crystal structure.

Groves, M.R.Dhanaraj, V.Badasso, M.Nugent, P.Pitts, J.E.Hoover, D.J.Blundell, T.L.

(1998) Protein Eng. 11: 833-840


  • PubMed Abstract: 
  • In the crystal structure of uncomplexed native chymosin, the beta-hairpin at the active site, known as 'the flap', adopts a different conformation from that of other aspartic proteinases. This conformation would prevent the mode of binding of substra ...

    In the crystal structure of uncomplexed native chymosin, the beta-hairpin at the active site, known as 'the flap', adopts a different conformation from that of other aspartic proteinases. This conformation would prevent the mode of binding of substrates/inhibitors generally found in other aspartic proteinase complexes. We now report the X-ray analysis of chymosin complexed with a reduced bond inhibitor CP-113972 ┬┐(2R,3S)-isopropyl 3-[(L-prolyl-p-iodo-L-phenylalanyl-S-methyl-cysteinyl)amino-4]-cyclohexy l-2-hydroxybutanoate┬┐ at 2.3 A resolution in a novel crystal form of spacegroup R32. The structure has been refined by restrained least-squares methods to a final R-factor of 0.19 for a total of 11 988 independent reflections in the resolution range 10 to 2.3 A. The extended beta-strand conformation of the inhibitor allows hydrogen bonds within the active site, while its sidechains make both electrostatic and hydrophobic interactions with residues lining the specificity pockets S4-->S1. The flap closes over the active site cleft in a way that closely resembles that of other previously determined aspartic proteinase inhibitor complexes. We conclude that the usual position and conformation of the flap found in other aspartic proteinases is available to native chymosin. The conformation observed in the native crystal form may result from intermolecular interactions between symmetry-related molecules in the crystal lattice.


    Related Citations: 
    • X-Ray Analyses of Aspartic Proteinases. Iv. Structure and Refinement at 2.2 A Resolution of Bovine Chymosin
      Newman, M.,Safro, M.,Frazao, C.,Khan, G.,Zdanov, A.,Tickle, I.J.,Blundell, T.L.,Andreeva, N.
      (1991) J.Mol.Biol. 221: 1295


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHYMOSIN
E
323Bos taurusMutation(s): 0 
Gene Names: CYM (CPC)
EC: 3.4.23.4
Find proteins for P00794 (Bos taurus)
Go to UniProtKB:  P00794
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE)
P
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000344
Query on PRD_000344
PNORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINEPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 132.780α = 90.00
b = 132.780β = 90.00
c = 81.950γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
CCP4data scaling
ROTAVATA)data scaling
AGROVATA/ROTAVATAdata reduction
RESTRAINrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    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: 2012-12-12
    Type: Other