1TM1

CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' WITH CHYMOTRYPSIN INHIBITOR 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Binding, Proteolytic, and Crystallographic Analyses of Mutations at the Protease-Inhibitor Interface of the Subtilisin BPN'/Chymotrypsin Inhibitor 2 Complex(,).

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

(2004) Biochemistry 43: 13648-13656

  • DOI: https://doi.org/10.1021/bi048797k
  • Primary Citation of Related Structures:  
    1TM1, 1TM3, 1TM4, 1TM5, 1TM7, 1TMG, 1TO1, 1TO2

  • PubMed Abstract: 

    A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues that interact with the inhibited enzyme subtilisin BPN', were studied to determine the relative importance of intermolecular contacts on either side of the scissile bond. Mutants were tested for inhibition of subtilisin, rates of hydrolysis by subtilisin, and ability to acylate subtilisin. Additionally, crystal structures of the mutant CI2 complexes with subtilisin were obtained. Ordered water molecules were found to play an important role in inhibitor recognition, and features of the crystal structures, in combination with biochemical data, support a transition-state stabilization role for the P(1) residue in subtilisin catalysis. Consistent with the proposed mechanism of inhibition, in which rapid acylation is followed by religation, leaving-group contacts with the enzyme were found to be more critical determinants of inhibition than acylating-group contacts in the mutants studied here.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Subtilisin BPN' precursorA [auth E]281Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: APR
EC: 3.4.21.62
UniProt
Find proteins for P00782 (Bacillus amyloliquefaciens)
Explore P00782 
Go to UniProtKB:  P00782
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00782
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
chymotrypsin inhibitor 2B [auth I]64Hordeum vulgare subsp. vulgareMutation(s): 0 
UniProt
Find proteins for Q40059 (Hordeum vulgare)
Explore Q40059 
Go to UniProtKB:  Q40059
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ40059
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
H [auth E],
I [auth E],
J [auth E],
K [auth E]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E,
F [auth E],
G [auth E]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth E]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.72α = 90
b = 93.72β = 90
c = 185.853γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
TRUNCATEdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description