9AWV | pdb_00009awv

Crystal structure of trypsin at 300 Kelvin with benzamidine (duplicate)

• PDB DOI: https://doi.org/10.2210/pdb9AWV/pdb

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


• Deposited: 2024-03-05 Released: 2025-03-12 
• Deposition Author(s): Lima, L.M.T.R., de Sa Ribeiro, F.
• Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.224 (DCC) 

Starting Model: experimental

Literature

Crystal structure of trypsin at 300 Kelvin with benzamidine (duplicate)

Lima, L.M.T.R., de Sa Ribeiro, F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 23.48 kDa 
• Atom Count: 1,719 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN (Subject of Investigation/LOI)	C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.224 (DCC) 

Diffraction Data: https://doi.org/10.18430/M39AWV

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.214	α = 90
b = 57.413	β = 90
c = 66.567	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Lima, L.M.T.R., de Sa Ribeiro, F.

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Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Author supporting evidence, Data collection, Other, Refinement description, Source and taxonomy, Structure summary