4ZYO

Crystal Structure of Human Integral Membrane Stearoyl-CoA Desaturase with Substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of human stearoyl-coenzyme A desaturase in complex with substrate.

Wang, H.Klein, M.G.Zou, H.Lane, W.Snell, G.Levin, I.Li, K.Sang, B.C.

(2015) Nat Struct Mol Biol 22: 581-585

  • DOI: 10.1038/nsmb.3049
  • Primary Citation of Related Structures:  
    4ZYO

  • PubMed Abstract: 
  • Stearoyl-coenzyme A desaturase-1 (SCD1) has an important role in lipid metabolism, and SCD1 inhibitors are potential therapeutic agents for the treatment of metabolic diseases and cancers. Here we report the 3.25-Å crystal structure of human SCD1 in complex with its substrate, stearoyl-coenzyme A, which defines the new SCD1 dimetal catalytic center and reveals the determinants of substrate binding to provide insights into the catalytic mechanism of desaturation of the stearoyl moiety ...

    Stearoyl-coenzyme A desaturase-1 (SCD1) has an important role in lipid metabolism, and SCD1 inhibitors are potential therapeutic agents for the treatment of metabolic diseases and cancers. Here we report the 3.25-Å crystal structure of human SCD1 in complex with its substrate, stearoyl-coenzyme A, which defines the new SCD1 dimetal catalytic center and reveals the determinants of substrate binding to provide insights into the catalytic mechanism of desaturation of the stearoyl moiety. The structure also provides a mechanism for localization of SCD1 in the endoplasmic reticulum: human SCD1 folds around a tight hydrophobic core formed from four long α-helices that presumably function as an anchor spanning the endoplasmic reticulum membrane. Furthermore, our results provide a framework for the rational design of pharmacological inhibitors targeting the SCD1 enzyme.


    Organizational Affiliation

    Department of Structural Biology and Core Sciences &Technology, Takeda California, San Diego, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-CoA desaturaseA318Homo sapiensMutation(s): 3 
Gene Names: SCD
EC: 1.14.19.1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Fatty Acid Desaturases
Protein: 
Stearoyl-coenzyme A desaturase (SCD1) in complex with substrate
Find proteins for O00767 (Homo sapiens)
Explore O00767 
Go to UniProtKB:  O00767
NIH Common Fund Data Resources
PHAROS:  O00767
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ST9
Query on ST9

Download Ideal Coordinates CCD File 
D [auth A]STEAROYL-COENZYME A
C39 H70 N7 O17 P3 S
SIARJEKBADXQJG-LFZQUHGESA-N
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
E [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.108α = 90
b = 134.108β = 90
c = 112.561γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references