3GID | pdb_00003gid

The biotin carboxylase (BC) domain of human Acetyl-CoA Carboxylase 2 (ACC2) in complex with Soraphen A

• PDB DOI: https://doi.org/10.2210/pdb3GID/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-05 Released: 2009-03-17 
• Deposition Author(s): Price, A., Kulathila, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.242 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Synthesis and characterization of a BODIPY-labeled derivative of Soraphen A that binds to acetyl-CoA carboxylase.

Raymer, B., Kavana, M., Price, A., Wang, B., Corcoran, L., Kulathila, R., Groarke, J., Mann, T.

(2009) Bioorg Med Chem Lett 19: 2804-2807

• PubMed: 19359168 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.107
• Primary Citation Related Structures: 
  3GID, 3GLK


• PubMed Abstract: 
  

  BODIPY-labeled Soraphen A derivative 4 was synthesized and characterized as an acetyl-CoA carboxylase (ACC) binder. Biophysical measurements indicate that the molecule binds in the biotin carboxylase domain where Soraphen A has been shown to bind. The fluorescent label of the BODIPY can be used to biophysically identify a compound that binds to the Soraphen A site of the biotin carboxylase domain versus the carboxytransferase domain of ACC.

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Organizational Affiliation: 
• Novartis Institutes for BioMedical Research, Cambridge, MA 02139, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 121.23 kDa 
• Atom Count: 7,413 
• Modeled Residue Count: 917 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA carboxylase 2	A, B	540	Homo sapiens	Mutation(s): 0  Gene Names: ACACB, ACC2, ACCB EC: 6.4.1.2 (PDB Primary Data), 6.3.4.14 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O00763 (Homo sapiens) Explore O00763  Go to UniProtKB:  O00763
PHAROS:  O00763 GTEx:  ENSG00000076555

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S1A	C [auth A], D [auth B]	SORAPHEN A C29 H44 O8 WPMGNXPRKGXGBO-OFQQMTDKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.242 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.339	α = 90
b = 141	β = 90
c = 123.615	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Price, A., Kulathila, R.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-12-10
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations