5YFN

Human isocitrate dehydrogenase 1 bound with isocitrate

• PDB DOI: https://doi.org/10.2210/pdb5YFN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-21 Released: 2017-10-25 
• Deposition Author(s): Nordlund, P., Chen, D., Jansson, A., Larsson, A.
• Funding Organization(s): Nanyang Technological University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Human isocitrate dehydrogenase 1 bound with isocitrate

Nordlund, P., Chen, D., Jansson, A., Larsson, A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 95.72 kDa 
• Atom Count: 6,724 
• Modelled Residue Count: 824 
• Deposited Residue Count: 842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	421	Homo sapiens	Mutation(s): 0  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
ICT	D [auth A], G [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N
K	F [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.56	α = 90
b = 92	β = 109.94
c = 138.835	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Nordlund, P., Chen, D., Jansson, A., Larsson, A.

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Funding Organization	Location	Grant Number
Nanyang Technological University	Singapore	M060080004

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description