6YDY

Cationic Trypsin in Complex with a D-Phe-Pro-benzylamine derivative

• PDB DOI: https://doi.org/10.2210/pdb6YDY/pdb

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


• Deposited: 2020-03-21 Released: 2021-03-31 
• Deposition Author(s): Ngo, K., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.185 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Cationic Trypsin in Complex with a D-Phe-Pro-benzylamine derivative

Sandner, A., Ngo, K., Schiebel, J., Marca, A., Schmidt, L., Steinmetzer, T., 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)

Macromolecule Content

• Total Structure Weight: 26.23 kDa 
• Atom Count: 1,887 
• Modelled Residue Count: 223 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic Trypsin	A	246	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K73 (Subject of Investigation/LOI)	C [auth A]	(2~{S})-~{N}-[[4-(aminomethyl)phenyl]methyl]-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]pyrrolidine-2-carboxamide C22 H28 N4 O2 MTUGEKUGFKKRIV-UXHICEINSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.185 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.6	α = 90
b = 54.6	β = 90
c = 108.536	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Ngo, K., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description