6Z2H | pdb_00006z2h

Citryl-CoA lyase module of human ATP citrate lyase in complex with (3S)-citryl-CoA.

• PDB DOI: https://doi.org/10.2210/pdb6Z2H/pdb

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


• Deposited: 2020-05-15 Released: 2021-05-26 
• Deposition Author(s): Verschueren, K.H.G., Verstraete, K.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Acetyl-CoA is produced by the citrate synthase homology module of ATP-citrate lyase.

Verstraete, K., Verschueren, K.H.G., Dansercoer, A., Savvides, S.N.

(2021) Nat Struct Mol Biol 28: 636-638

• PubMed: 34294920 
• DOI: https://doi.org/10.1038/s41594-021-00624-3
• Primary Citation Related Structures: 
  6Z2H, 6ZNW

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Organizational Affiliation: 
• VIB-UGent Center for Inflammation Research, Ghent, Belgium. [e-mail].
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. [e-mail].
VIB-UGent Center for Inflammation Research, Ghent, Belgium.
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
VIB-UGent Center for Inflammation Research, Ghent, Belgium. [e-mail].
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 124.74 kDa 
• Atom Count: 9,165 
• Modeled Residue Count: 1,049 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-citrate synthase	A, B, C, D	270	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
Q5B (Subject of Investigation/LOI)	E [auth A], H [auth C], K [auth D]	(3S)-citryl-Coenzyme A C27 H42 N7 O22 P3 S IHVFHZGGMJDGGZ-VPXVXCNZSA-N
ACO (Subject of Investigation/LOI)	G [auth A], J [auth C]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
OAA (Subject of Investigation/LOI)	F [auth A], I [auth C]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.436	α = 90
b = 114.271	β = 90
c = 144.108	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Verschueren, K.H.G., Verstraete, K.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0G0619N

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references
• Version 1.2: 2021-08-25
  Changes: Database references
• Version 1.3: 2021-09-22
  Changes: Data collection, Database references
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-01-24
  Changes: Refinement description