5GV5

Crystal structure of Candida antarctica Lipase B with active Ser105 modified with a phosphonate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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Literature

Structural and Experimental Evidence for the Enantiomeric Recognition toward a Bulky sec-Alcohol by Candida antarctica Lipase B

Park, K.Kim, S.Park, J.Joe, S.Min, B.Oh, J.Song, J.Park, S.Y.Park, S.Lee, H.

(2016) ACS Catal 6: 7458-7465


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipase BABCDEFGH317Moesziomyces antarcticusMutation(s): 0 
EC: 3.1.1.3
Find proteins for M9MDK9 (Pseudozyma antarctica (strain T-34))
Explore M9MDK9 
Go to UniProtKB:  M9MDK9
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, K
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, L, M, N, O, P
2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.462α = 90
b = 123.222β = 96.2
c = 150.316γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2016-09-02 
  • Released Date: 2017-09-13 
  • Deposition Author(s): Park, S.Y., Lee, H.

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary