4X2Q | pdb_00004x2q

Crystal Structure of Human Aldehyde Dehydrogenase, ALDH1a2

• PDB DOI: https://doi.org/10.2210/pdb4X2Q/pdb

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


• Deposited: 2014-11-26 Released: 2015-12-02 
• Deposition Author(s): Stenkamp, R.E., Le Trong, I., Amory, J.K., Paik, J., Goldstein, A.S.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.313 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: experimental

Literature

Synthesis and In Vitro Testing of Bisdichloroacetyldiamine Analogs for Use as a Reversible Male Contraceptive

Goldstein, A.S., Paik, J., Moreb, J., Haenisch, M., Le Trong, I., Stenkamp, R.E., Petrie, A.G., Smith, N., Mallochowski, W.P., Amory, J.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 224.74 kDa 
• Atom Count: 14,765 
• Modeled Residue Count: 1,892 
• Deposited Residue Count: 2,016 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal dehydrogenase 2	A, B, C, D	504	Homo sapiens	Mutation(s): 0  Gene Names: ALDH1A2, RALDH2 EC: 1.2.1.36
UniProt & NIH Common Fund Data Resources
Find proteins for O94788 (Homo sapiens) Explore O94788  Go to UniProtKB:  O94788
PHAROS:  O94788 GTEx:  ENSG00000128918

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.313 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.597	α = 90
b = 140.508	β = 90
c = 164.452	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Stenkamp, R.E., Le Trong, I., Amory, J.K., Paik, J., Goldstein, A.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	U01 HD060488
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	U54 HD42454

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description