3PFF | pdb_00003pff

Truncated human atp-citrate lyase with ADP and tartrate bound

• PDB DOI: https://doi.org/10.2210/pdb3PFF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-28 Released: 2011-10-12 
• Deposition Author(s): Fraser, M.E., Sun, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Models: experimental

Literature

ADP-Mg2+ bound to the ATP-grasp domain of ATP-citrate lyase.

Sun, T., Hayakawa, K., Fraser, M.E.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1168-1172

• PubMed: 22102020 
• DOI: https://doi.org/10.1107/S1744309111028363
• Primary Citation Related Structures: 
  3PFF


• PubMed Abstract: 
  

  Human ATP-citrate lyase (EC 2.3.3.8) is the cytoplasmic enzyme that catalyzes the production of acetyl-CoA from citrate, CoA and ATP. The amino-terminal portion of the enzyme, containing residues 1-817, was crystallized in the presence of tartrate, ATP and magnesium ions. The crystals diffracted to 2.3 Å resolution. The structure shows ADP-Mg(2+) bound to the domain that possesses the ATP-grasp fold. The structure demonstrates that this crystal form could be used to investigate the structures of complexes with inhibitors of ATP-citrate lyase that bind at either the citrate- or ATP-binding site.

---

Organizational Affiliation: 
• Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.44 kDa 
• Atom Count: 6,122 
• Modeled Residue Count: 735 
• Deposited Residue Count: 829 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-citrate synthase	A	829	Homo sapiens	Mutation(s): 0  Gene Names: ACLY EC: 2.3.3.8
UniProt & NIH Common Fund Data Resources
Find proteins for P53396 (Homo sapiens) Explore P53396  Go to UniProtKB:  P53396
PHAROS:  P53396 GTEx:  ENSG00000131473

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.54	α = 90
b = 61.7	β = 125.47
c = 107.98	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Fraser, M.E., Sun, T.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary