3VPK | pdb_00003vpk

Crystal Structure of 6-Guanidinohexanoyl Trypsin

• PDB DOI: https://doi.org/10.2210/pdb3VPK/pdb

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


• Deposited: 2012-03-05 Released: 2012-05-23 
• Deposition Author(s): Masuda, Y., Nitanai, Y., Mizutani, R., Noguchi, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated

Masuda, Y., Nitanai, Y., Mizutani, R., Noguchi, S.

(2012) Proteins 

• PubMed: 23161653 
• DOI: https://doi.org/10.1002/prot.24206
• Primary Citation Related Structures: 
  3VPK


• PubMed Abstract: 
  

  The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optimum reaction pH, at 1.94 Å resolution. In this structure, three water molecules are observed around the catalytic site. One acts as a nucleophile to attack the acyl carbonyl carbon while the other two waters fix the position of the catalytic water through a hydrogen bond. When the acyl carbonyl oxygen oscillates thermally, the water assumes an appropriate angle to catalyze the deacylation.

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Organizational Affiliation: 
• Nuclear, Biological and Chemical Detection Technology Section, Human Oriented Systems Division, Advanced Defense Technology Center, Technical Research and Development Institute, Ministry of Defense, Meguro, Tokyo 153-8630, Japan. [e-mail]

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: 23.7 kDa 
• Atom Count: 1,811 
• 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
GHS	B [auth A]	6-carbamimidamidohexanoic acid C7 H15 N3 O2 NSDYIDKTTPXCRH-UHFFFAOYSA-N
E4B	D [auth A]	ethyl 4-hydroxybenzoate C9 H10 O3 NUVBSKCKDOMJSU-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.779	α = 90
b = 61.05	β = 90
c = 69.664	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Masuda, Y., Nitanai, Y., Mizutani, R., Noguchi, S.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2013-02-06
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary