4KGB

Structure of succinyl-CoA: 3-ketoacid CoA transferase from Drosophila melanogaster

• PDB DOI: https://doi.org/10.2210/pdb4KGB/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-29 Released: 2013-10-23 
• Deposition Author(s): Wang, Y.C., Shi, Z.B., Zhang, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.261 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Structure of succinyl-CoA:3-ketoacid CoA transferase from Drosophila melanogaster.

Zhang, M., Xu, H.Y., Wang, Y.C., Shi, Z.B., Zhang, N.N.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1089-1093

• PubMed: 24100554 
• DOI: https://doi.org/10.1107/S1744309113024986
• Primary Citation of Related Structures:  
  4KGB


• PubMed Abstract: 
  

  Succinyl-CoA:3-ketoacid CoA transferase (SCOT) plays a crucial role in ketone-body metabolism. SCOT from Drosophila melanogaster (DmSCOT) was purified and crystallized. The crystal structure of DmSCOT was determined at 2.64 Å resolution and belonged to space group P212121, with unit-cell parameters a=76.638, b=101.921, c=122.457 Å, α=β=γ=90°. Sequence alignment and structural analysis identified DmSCOT as a class I CoA transferase. Compared with Acetobacter aceti succinyl-CoA:acetate CoA transferase, DmSCOT has a different substrate-binding pocket, which may explain the difference in their substrate specificities.

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Organizational Affiliation: 

School of Life Science, Anhui University, Hefei 230026, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.53 kDa 
• Atom Count: 6,931 
• Modelled Residue Count: 930 
• Deposited Residue Count: 974 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA:3-ketoacid-coenzyme A transferase	A, B	487	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG1140, Dmel_CG1140 EC: 2.8.3.5
UniProt
Find proteins for Q9W058 (Drosophila melanogaster) Explore Q9W058  Go to UniProtKB:  Q9W058

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.261 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.638	α = 90
b = 101.921	β = 90
c = 122.457	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Wang, Y.C., Shi, Z.B., Zhang, M.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description