1Y3D

Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 R67A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2

Radisky, E.S.Lu, C.J.Kwan, G.Koshland Jr., D.E.

(2005) Biochemistry 44: 6823-6830

  • DOI: 10.1021/bi047301w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin ...

    A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues involved in intramolecular interactions that shape and constrain the binding loop, were studied to determine their relative importance for inhibition of the serine protease subtilisin BPN', and for resistance of the inhibitor to proteolysis. These functional properties were investigated in tandem with the crystal structures of the mutant inhibitor-enzyme complexes. A dense hydrogen bonding network that supports the binding loop in the vicinity of the scissile bond was found to be important both for enzyme affinity and for stability to proteolysis. Structural analysis, in combination with biochemical measurements, allows differentiation of the structural components most important for resistance to proteolysis and/or binding. The most critical participating residues in the network were found to be Thr-58, Glu-60, Arg-65, and Gly-83. Glu-60 is more important for resistance to proteolysis than for binding, while Arg-65 and two other Arg residues play a greater role in binding than in resistance to proteolysis. Structural comparisons reveal a wide variety of subtle conformational changes in response to mutation, with built-in robustness in the hydrogen bond network, such that loss of one contact is compensated by other new contacts.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
subtilisin BPN'
E
281Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00782 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00782
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
chymotrypsin inhibitor 2
I
64Hordeum vulgareMutation(s): 1 
Gene Names: Ica-2
Find proteins for Q40059 (Hordeum vulgare)
Go to UniProtKB:  Q40059
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
E, I
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.147 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.265α = 90.00
b = 94.265β = 90.00
c = 185.574γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
EPMRphasing
REFMACrefinement
TRUNCATEdata reduction
MOSFLMdata reduction
TRUNCATEdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description