3B29

Human leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Seleno-detergent MAD phasing of leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside

Saino, H.Ago, H.Ukita, Y.Miyano, M.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1666-1673

  • DOI: 10.1107/S1744309111042345
  • Primary Citation of Related Structures:  
    3B29

  • PubMed Abstract: 
  • Dodecyl-β-D-selenomaltoside (SeDDM) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-D-maltoside. Seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography ...

    Dodecyl-β-D-selenomaltoside (SeDDM) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-D-maltoside. Seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography. Crystals of a nuclear membrane-embedded enzyme, leukotriene C(4) synthase (LTC(4)S), in complex with SeDDM were prepared and a multiwavelength anomalous diffraction (MAD) experiment was performed. The SeDDM in the LTC(4)S crystal exhibited sufficient anomalous diffraction for determination of the structure using MAD phasing.


    Organizational Affiliation

    Structural Biophysics Laboratory, RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leukotriene C4 synthaseA156Homo sapiensMutation(s): 0 
Gene Names: LTC4S
EC: 4.4.1.20 (PDB Primary Data), 2.5.1 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens)
Explore Q16873 
Go to UniProtKB:  Q16873
PHAROS:  Q16873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16873
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LSM
Query on LSM

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
dodecyl 4-O-alpha-D-glucopyranosyl-1-seleno-beta-D-glucopyranoside
C24 H46 O10 Se
MEIBWTYMLPEGMV-ALYNCGSASA-N
 Ligand Interaction
GSH
Query on GSH

Download Ideal Coordinates CCD File 
B [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.594α = 90
b = 168.594β = 90
c = 168.594γ = 90
Software Package:
Software NamePurpose
BSSdata collection
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references