12VT | pdb_000012vt

Y318A Human Aconitate Decarboxylase 1 mutant, apo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 
    0.202 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Robust structural, kinetic and biophysical characterization of wild-type human ACOD1, selected mutants and their interaction with citraconate.

Runge, B.Oktay, H.Fucci, I.J.Merten, E.M.Tarasov, S.G.Fan, L.Monteiro, D.C.F.

(2026) J Struct Biol X 14: 100157-100157

  • DOI: https://doi.org/10.1016/j.yjsbx.2026.100157
  • Primary Citation Related Structures: 
    12UX, 12VD, 12VQ, 12VT, 12VW

  • PubMed Abstract: 

    Aconitate decarboxylase 1, an enzyme member of the MmgE-PrpD family of proteins, has gained significant attention in the last decade as a therapeutic target for cancer and inflammatory diseases. Its product, itaconate, is a multifunctional metabolite shown to drive several disease states. Though extensively studied in cellulo and in vivo , this protein is biochemically and mechanistically under characterized and although a family of inhibitors has been described, no ligand-bound structures have yet been determined. In this work we present a thorough structural investigation that yielded the first ligand-bound structure of this protein family, which required the generation of artifact-free apo crystals. We also developed a novel, low-consumption, robust kinetic assay and investigated active site and allosteric mutants to further elucidate structural and dynamic activity relationships of this protein.


  • Organizational Affiliation
    • Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.

Macromolecule Content 

  • Total Structure Weight: 101.39 kDa 
  • Atom Count: 8,004 
  • Modeled Residue Count: 916 
  • Deposited Residue Count: 924 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cis-aconitate decarboxylase
A, B
462Homo sapiensMutation(s): 1 
Gene Names: ACOD1IRG1
EC: 4.1.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for A6NK06 (Homo sapiens)
Explore A6NK06 
Go to UniProtKB:  A6NK06
PHAROS:  A6NK06
GTEx:  ENSG00000102794 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6NK06
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.889α = 90
b = 110.165β = 90
c = 76.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-19
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Database references