5YFM | pdb_00005yfm

Human isocitrate dehydrogenase 1 bound with NADP

• PDB DOI: https://doi.org/10.2210/pdb5YFM/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: 2.40 Å
• R-Value Free: 
  0.239 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Human isocitrate dehydrogenase 1 bound with NADP

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 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 142.46 kDa 
• Atom Count: 10,322 
• Modeled Residue Count: 1,226 
• Deposited Residue Count: 1,242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B, C	414	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A], F [auth B], H [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MG	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.239 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.02	α = 90
b = 85.58	β = 98.08
c = 86.07	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
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