2AGE

Succinyl-AAPR-trypsin acyl-enzyme at 1.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2AGE/pdb

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


• Deposited: 2005-07-26 Released: 2006-05-16 
• Deposition Author(s): Radisky, E.S., Lee, J.M., Lu, C.J., Koshland Jr., D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.138 
• R-Value Work: 0.119 
• R-Value Observed: 0.120 

Starting Model: experimental

Literature

Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates

Radisky, E.S., Lee, J.M., Lu, C.J., Koshland Jr., D.E.

(2006) Proc Natl Acad Sci U S A 103: 6835-6840

• PubMed: 16636277 
• DOI: https://doi.org/10.1073/pnas.0601910103
• Primary Citation of Related Structures:  
  2AGE, 2AGG, 2AGI, 2AH4


• PubMed Abstract: 
  

  Atomic resolution structures of trypsin acyl-enzymes and a tetrahedral intermediate analog, along with previously solved structures representing the Michaelis complex, are used to reconstruct events in the catalytic cycle of this classic serine protease. Structural comparisons provide insight into active site adjustments involved in catalysis. Subtle motions of the catalytic serine and histidine residues coordinated with translation of the substrate reaction center are seen to favor the forward progress of the acylation reaction. The structures also clarify the attack trajectory of the hydrolytic water in the deacylation reaction.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.86 kDa 
• Atom Count: 2,092 
• Modelled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A [auth X]	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
succinyl-Ala-Ala-Pro-Arg	B [auth A]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OAR	B [auth A]	PEPTIDE-LIKE	C6 H16 N4 O		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.138 
• R-Value Work: 0.119 
• R-Value Observed: 0.120 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.948	α = 90
b = 63.72	β = 90
c = 69.008	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
EPMR	phasing
REFMAC	refinement
CCP4	data scaling
TRUNCATE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-16 
Deposition Author(s): Radisky, E.S., Lee, J.M., Lu, C.J., Koshland Jr., D.E.

Revision History  

• Version 1.0: 2006-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2024-04-24
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary