1LLF

Cholesterol Esterase (Candida Cylindracea) Crystal Structure at 1.4A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.142 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Three-dimensional structure of homodimeric cholesterol esterase-ligand complex at 1.4 A resolution.

Pletnev, V.Addlagatta, A.Wawrzak, Z.Duax, W.

(2003) Acta Crystallogr D Biol Crystallogr 59: 50-56

  • DOI: https://doi.org/10.1107/s0907444902018851
  • Primary Citation of Related Structures:  
    1LLF

  • PubMed Abstract: 

    The three-dimensional structure of a Candida cylindracea cholesterol esterase (ChE) homodimer (534 x 2 amino acids) in complex with a ligand of proposed formula C(23)H(48)O(2) has been determined at 1.4 A resolution in space group P1 using synchrotron low-temperature data. The structure refined to R = 0.136 and R(free) = 0.169 and has revealed new stereochemical details in addition to those detected for the apo- and holo-forms at 1.9 and 2.0 A resolution, respectively [Ghosh et al. (1995), Structure, 3, 279-288]. The cholesterol esterase structure is a dimer with four spatially separated interfacial contact areas and two symmetry-related pairs of openings to an internal intradimer cavity. Hydrophobic active-site gorges in each subunit face each other across a central interfacial cavity. The ChE subunits have carbohydrate chains attached to their Asn314 and Asn351 residues, with two ordered N-acetyl-D-glucosoamine moieties visible at each site. The side chains of 14 residues have two alternative conformations with occupancy values of 0.5 +/- 0.2. For each subunit the electron density in the enzyme active-site gorge is well modeled by a C(23)-chain fatty acid.


  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase 3
A, B
534Limtongozyma cylindraceaMutation(s): 0 
EC: 3.1.1.3
UniProt
Find proteins for Q6S5M9 (Limtongozyma cylindracea)
Explore Q6S5M9 
Go to UniProtKB:  Q6S5M9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6S5M9
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.142 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.461α = 92.71
b = 58.477β = 97.48
c = 89.515γ = 109.38
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary