1TO2

crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59K, in pH 9 cryosoak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/bi048797k
  • Primary Citation of Related Structures:  1TM1, 1TM3, 1TM4, 1TM5, 1TM7, 1TMG, 1TO1

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subtilisin BPN'
E
281Bacillus amyloliquefaciensGene 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 vulgareGene 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

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E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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

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E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.168 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.671α = 90.00
b = 93.671β = 90.00
c = 185.920γ = 120.00
Software Package:
Software NamePurpose
EPMRphasing
REFMACrefinement
TRUNCATEdata scaling
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    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