5MNM | pdb_00005mnm

Cationic trypsin in complex with benzylamine (at 295 K)

• PDB DOI: https://doi.org/10.2210/pdb5MNM/pdb

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


• Deposited: 2016-12-13 Released: 2018-01-17 
• Deposition Author(s): Schiebel, J., Heine, A., Klebe, G.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.112 (Depositor), 0.110 (DCC) 
• R-Value Work: 
  0.101 (Depositor), 0.100 (DCC) 
• R-Value Observed: 
  0.101 (Depositor) 

Starting Model: experimental

Literature

Cationic trypsin in complex with benzylamine (at 295 K)

Schiebel, 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)

Macromolecule Content 

• Total Structure Weight: 23.76 kDa 
• Atom Count: 1,979 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ABN	F [auth A]	BENZYLAMINE C7 H9 N WGQKYBSKWIADBV-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.112 (Depositor), 0.110 (DCC) 
• R-Value Work:  0.101 (Depositor), 0.100 (DCC) 
• R-Value Observed: 0.101 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.841	α = 90
b = 58.334	β = 90
c = 67.781	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Schiebel, J., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
European Research Council		268145-DrugProfilBind

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary