4ABI | pdb_00004abi

Co-complex structure of bovine trypsin with a modified Bowman-Birk inhibitor (PtA)SFTI-1(1,14), that was 1,4-disubstituted with a 1,2,3- trizol to mimic a trans amide bond

• PDB DOI: https://doi.org/10.2210/pdb4ABI/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Bos taurus, synthetic construct
• Mutation(s): No 


• Deposited: 2011-12-08 Released: 2012-03-07 
• Deposition Author(s): Schmelz, S., Empting, M., Tischler, M., Nasu, D., Heinz, D., Kolmar, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Braces for the Peptide Backbone: Insights Into Structure-Activity Relation-Ships of Protease Inhibitor Mimics with Locked Amide Conformations

Tischler, M., Nasu, D., Empting, M., Schmelz, S., Heinz, D., Rottmann, P., Kolmar, H., Buntkowsky, G., Tietze, D., Avrutina, O.

(2012) Angew Chem Int Ed Engl 51: 3708

• PubMed: 22374650 
• DOI: https://doi.org/10.1002/anie.201108983
• Primary Citation of Related Structures:  
  4ABI, 4ABJ

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Organizational Affiliation: 
• Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.95 kDa 
• Atom Count: 2,201 
• Modeled Residue Count: 234 
• Deposited Residue Count: 236 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATIONIC TRYPSIN	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PTA-SFTI INHIBITOR	B	13	synthetic construct	Mutation(s): 0
UniProt
Find proteins for Q4GWU5 (Helianthus annuus) Explore Q4GWU5  Go to UniProtKB:  Q4GWU5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	N [auth A], O [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMF	D [auth A], E [auth A], F [auth A]	DIMETHYLFORMAMIDE C3 H7 N O ZMXDDKWLCZADIW-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000842	B	PTA-SFTI INHIBITOR	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.1	α = 90
b = 63.2	β = 90
c = 69.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
DENZO	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Schmelz, S., Empting, M., Tischler, M., Nasu, D., Heinz, D., Kolmar, H.

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Other
• Version 1.2: 2012-05-16
  Changes: Other
• Version 1.3: 2012-11-14
  Changes: Database references
• Version 1.4: 2012-11-30
  Changes: Other
• Version 1.5: 2017-06-28
  Changes: Data collection
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-12-20
  Changes: Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary