8VHC

Crystal Structure of Human IDH1 R132Q in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb8VHC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-12-31 Released: 2024-04-24 
• Deposition Author(s): Mealka, M., Sohl, C.D., Huxford, T.
• Funding Organization(s): American Cancer Society, National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.240 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Active site remodeling in tumor-relevant IDH1 mutants drive distinct kinetic features and possible resistance mechanisms

Mealka, M., Sohl, C.D., Huxford, T.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 98.87 kDa 
• Atom Count: 6,488 
• Modelled Residue Count: 794 
• Deposited Residue Count: 860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	430	Homo sapiens	Mutation(s): 1  Gene Names: IDH1, PICD EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens) Explore O75874  Go to UniProtKB:  O75874
PHAROS:  O75874 GTEx:  ENSG00000138413

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	D [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SO4	G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.240 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.884	α = 90
b = 82.884	β = 90
c = 303.926	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Mealka, M., Sohl, C.D., Huxford, T.

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Funding Organization	Location	Grant Number
American Cancer Society	United States	RSG-19-075-01-TBE
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 GM137773

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release