3BX1 | pdb_00003bx1

Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.239 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3BX1

This is version 1.3 of the entry. See complete history

Literature

Structural and Mutational Analyses of the Interaction between the Barley alpha-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition

Micheelsen, P.O.Vevodova, J.De Maria, L.Ostergaard, P.R.Friis, E.P.Wilson, K.Skjot, M.

(2008) J Mol Biology 380: 681-690

  • DOI: https://doi.org/10.1016/j.jmb.2008.05.034
  • Primary Citation Related Structures: 
    3BX1

  • PubMed Abstract: 

    Subtilisins represent a large class of microbial serine proteases. To date, there are three-dimensional structures of proteinaceous inhibitors from three families in complex with subtilisins in the Protein Data Bank. All interact with subtilisin via an exposed loop covering six interacting residues. Here we present the crystal structure of the complex between the Bacillus lentus subtilisin Savinase and the barley alpha-amylase/subtilisin inhibitor (BASI). This is the first reported structure of a cereal Kunitz-P family inhibitor in complex with a subtilisin. Structural analysis revealed that BASI inhibits Savinase in a novel way, as the interacting loop is shorter than loops previously reported. Mutational analysis showed that Thr88 is crucial for the inhibition, as it stabilises the interacting loop through intramolecular interactions with the BASI backbone.


  • Organizational Affiliation
    • Research and Development, Novozymes A/S, Krogshøjvej 36, 2880 Bagsvaerd, Denmark. pnmi@novozymes.com

Macromolecule Content 

  • Total Structure Weight: 94.4 kDa 
  • Atom Count: 7,228 
  • Modeled Residue Count: 900 
  • Deposited Residue Count: 900 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Subtilisin Savinase
A, B
269N/AMutation(s): 0 
EC: 3.4.21.62
UniProt
Find proteins for P29600 (Lederbergia lenta)
Explore P29600 
Go to UniProtKB:  P29600
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29600
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-amylase/subtilisin inhibitorC [auth D],
D [auth C]
181Hordeum vulgareMutation(s): 0 
UniProt
Find proteins for P07596 (Hordeum vulgare)
Explore P07596 
Go to UniProtKB:  P07596
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07596
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
CA [auth D],
E [auth A],
GA [auth C],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
DA [auth D]
EA [auth D]
F [auth A]
FA [auth D]
G [auth A]
DA [auth D],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
LA [auth C]
Q [auth A]
R [auth A]
AA [auth B],
BA [auth B],
LA [auth C],
Q [auth A],
R [auth A],
S [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.239 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.637α = 90
b = 100.637β = 90
c = 216.242γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary