6Z2H

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-citrate synthase
A, B, C, D
270Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53396
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5B (Subject of Investigation/LOI)
Query on Q5B

Download Ideal Coordinates CCD File 
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)
Query on ACO

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
OAA (Subject of Investigation/LOI)
Query on OAA

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.436α = 90
b = 114.271β = 90
c = 144.108γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0G0619N

Revision History  (Full details and data files)

  • 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