2SIC

REFINED CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' AND STREPTOMYCES SUBTILISIN INHIBITOR AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined crystal structure of the complex of subtilisin BPN' and Streptomyces subtilisin inhibitor at 1.8 A resolution.

Takeuchi, Y.Satow, Y.Nakamura, K.T.Mitsui, Y.

(1991) J.Mol.Biol. 221: 309-325


  • PubMed Abstract: 
  • The crystal structure of subtilisin BPN' complexed with a proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor) was refined at 1.8 A resolution to an R-factor of 0.177 with a root-mean-square deviation from ideal bond lengths of 0.014 A. Th ...

    The crystal structure of subtilisin BPN' complexed with a proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor) was refined at 1.8 A resolution to an R-factor of 0.177 with a root-mean-square deviation from ideal bond lengths of 0.014 A. The work finally established that the SSI-subtilisin complex is a Michaelis complex with a distance between the O gamma of active Ser221 and the carbonyl carbon of the scissile peptide bond being an intermediate value between a covalent bond and a van der Waals' contact, 2.7 A. This feature, as well as the geometry of the catalytic triad and the oxyanion hole, is coincident with that found in other highly refined crystal structures of the complex of subtilisin Novo, subtilisin Carlsberg, bovine trypsin or Streptomyces griseus protease B with their proteinaceous inhibitors. The enzyme-inhibitor beta-sheet interaction is composed of two separate parts: that between the P1-P3 residues of SSI and the 125-127 chain segment (the "S1-3 site") of subtilisin and that between the P4-P6 residues of SSI and th 102-104 chain segment (the "S4-6 site") of subtilisin. The latter beta-interaction is unique to subtilisin. In contrast, the beta-sheet interaction previously found in the complex of subtilisin Novo and chymotrypsin inhibitor 2 or in the complex of subtilisin Carlsberg and Eglin C is distinct from the present complex in that the two types of beta-interactions are not separate. As for the flexibility of the molecules comprising the present complex, the following observations were made by comparing the B-factors for free and complexed SSI and comparing those for free and complexed subtilisin BPN'. The rigidification of the component molecules upon complex formation occurs in a very localized region: in SSI, the "primary" and "secondary" contact regions and the flanking region; in subtilisin BPN', the S1-3 and S4-6 sites and the flanking region.


    Related Citations: 
    • Crystal Structure at 2.6 Angstroms Resolution of the Complex of Subtilisin with Bpn' with Streptomyces Subtilisin Inhibitor
      Hirono, S.,Akagawa, H.,Mitsui, Y.,Iitaka, Y.
      (1984) J.Mol.Biol. 178: 389
    • Crystal Structure of the Complex of Subtilisin Bpn' with its Protein Inhibitor Streptomyces Subtilisin Inhibitor
      Hirono, S.,Nakamura, K.T.,Iitaka, Y.,Mitsui, Y.
      (1979) J.Mol.Biol. 131: 855
    • Crystal Structures of Streptomyces Subtilisin Inhibitor and its Complex with Subtilisin Bpn'
      Mitsui, Y.,Satow, Y.,Watanabe, Y.,Hirono, S.,Iitaka, Y.
      (1979) Nature 277: 447


    Organizational Affiliation

    Pharmaceutical Research Center, Meiji Seika Kaisha, Ltd., Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUBTILISIN BPN'
E
275Bacillus 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
STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
I
107Streptomyces albogriseolusMutation(s): 0 
Gene Names: ssi
Find proteins for P01006 (Streptomyces albogriseolus)
Go to UniProtKB:  P01006
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.230α = 90.00
b = 185.900β = 90.00
c = 69.510γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other