2EEK | pdb_00002eek

Crystal structure of Atlantic cod trypsin complexed with benzamidine

• PDB DOI: https://doi.org/10.2210/pdb2EEK/pdb

• Classification: HYDROLASE
• Organism(s): Gadus morhua
• Mutation(s): No 


• Deposited: 2007-02-15 Released: 2008-02-19 
• Deposition Author(s): Iyaguchi, D., Toyota, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.224 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Atlantic cod trypsin complexed with benzamidine

Iyaguchi, D., Toyota, E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.77 kDa 
• Atom Count: 1,775 
• Modeled Residue Count: 220 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin-1	A	220	Gadus morhua	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P16049 (Gadus morhua) Explore P16049  Go to UniProtKB:  P16049

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	D [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.224 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.213	α = 90
b = 59.184	β = 90
c = 63.736	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Iyaguchi, D., Toyota, E.

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary