7QIQ

CRYSTAL STRUCTURE OF THE P1 aminobutanoic acid (ABU) BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Fluorine-induced polarity increases inhibitory activity of BPTI towards chymotrypsin.

Leppkes, J.Dimos, N.Loll, B.Hohmann, T.Dyrks, M.Wieseke, A.Keller, B.G.Koksch, B.

(2022) RSC Chem Biol 3: 773-782

  • DOI: 10.1039/d2cb00018k
  • Primary Citation of Related Structures:  
    7QIQ, 7QIR, 7QIS, 7QIT

  • PubMed Abstract: 
  • Substituting the P 1 position in bovine pancreatic trypsin inhibitor (BPTI) is known to heavily influence its inhibitory activity towards serine proteases. Side-chain fluorinated aliphatic amino acids have been shown to alter numerous properties of peptides and proteins and thus are of interest in the context of BPTI ...

    Substituting the P 1 position in bovine pancreatic trypsin inhibitor (BPTI) is known to heavily influence its inhibitory activity towards serine proteases. Side-chain fluorinated aliphatic amino acids have been shown to alter numerous properties of peptides and proteins and thus are of interest in the context of BPTI. In our study, we systematically investigated the site-specific incorporation of non-canonical amino acids into BPTI by microwave-assisted solid-phase peptide synthesis (SPPS). Inhibitor activity of the variants was tested towards the serine protease α-chymotrypsin. We observed enhanced inhibition of two fluorinated BPTIs compared to wild type and hydrocarbon variants. To further investigate the complexes, we performed X-ray structure analysis. Our findings underline the power fluorine offers as a tool in protein engineering to beneficially alter the effects on phenomena as protein-protein interactions.


    Organizational Affiliation

    Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany beate.koksch@fu-berlin.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chymotrypsin A chain AA, E13Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus)
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Go to UniProtKB:  P00766
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00766
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chymotrypsin A chain BB, F131Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
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UniProt GroupP00766
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chymotrypsin A chain CC, G97Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
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Go to UniProtKB:  P00766
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UniProt GroupP00766
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Pancreatic trypsin inhibitorD, H58Bos taurusMutation(s): 1 
UniProt
Find proteins for P00974 (Bos taurus)
Explore P00974 
Go to UniProtKB:  P00974
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UniProt GroupP00974
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
GA [auth D],
HA [auth D],
AA [auth C],
BA [auth C],
CA [auth C],
GA [auth D],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth D],
O [auth B],
OA [auth F],
P [auth B],
PA [auth F],
VA [auth G],
WA [auth G],
ZA [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth D],
EA [auth D],
FA [auth D],
I [auth B],
J [auth B],
DA [auth D],
EA [auth D],
FA [auth D],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
LA [auth F],
M [auth B],
MA [auth F],
N [auth B],
NA [auth F],
Q [auth C],
QA [auth G],
R [auth C],
RA [auth G],
S [auth C],
SA [auth G],
T [auth C],
TA [auth G],
U [auth C],
UA [auth G],
V [auth C],
W [auth C],
X [auth C],
XA [auth H],
Y [auth C],
YA [auth H],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
D, H L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 61
  • Diffraction Data DOI: 10.18430/M37QIQ Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.435α = 90
b = 100.435β = 90
c = 206.331γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyProject-ID 387284271

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references