2AGI

The leupeptin-trypsin covalent complex at 1.14 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1073/pnas.0601910103
  • Primary Citation of Related Structures:  
    2AGI, 2AH4, 2AGG, 2AGE

  • 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 prote ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
beta-trypsinX223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
leupeptinA4Streptomyces roseusMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AR7
Query on AR7
APEPTIDE-LIKEC6 H17 N4 O2ARG
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000216
Query on PRD_000216
ALEUPEPTINOligopeptide /  Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.888α = 90
b = 63.562β = 90
c = 69.102γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
EPMRphasing
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-10-11
    Changes: Refinement description