6YIW | pdb_00006yiw

Trypsin inhibitor in complex with bovine trypsin

• PDB DOI: https://doi.org/10.2210/pdb6YIW/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2020-04-01 Released: 2020-12-02 
• Deposition Author(s): Badran, M.J., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

Trypsin inhibitor in complex with bovine trypsin

Badran, M.J., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 24.1 kDa 
• Atom Count: 2,129 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F05 (Subject of Investigation/LOI)	J [auth A]	1H-isoindol-3-amine C8 H8 N2 MTKKGHVQPVOXIL-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.258	α = 90
b = 58.156	β = 90
c = 66.863	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Badran, M.J., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 2.0: 2021-03-03
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-10-09
  Changes: Structure summary