3INL | pdb_00003inl

Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with agonist Alda-1

PDB DOI: https://doi.org/10.2210/pdb3INL/pdb

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

Deposited: 2009-08-12 Released: 2010-01-12
Deposition Author(s): Perez-Miller, S., Hurley, T.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.168 (Depositor), 0.135 (DCC)
R-Value Work:
0.136 (Depositor), 0.137 (DCC)
R-Value Observed:
0.136 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant.

Perez-Miller, S., Younus, H., Vanam, R., Chen, C.H., Mochly-Rosen, D., Hurley, T.D.

(2010) Nat Struct Mol Biol 17: 159-164

PubMed: 20062057 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1737
Primary Citation Related Structures:
3INJ, 3INL

PubMed Abstract:
In approximately one billion people, a point mutation inactivates a key detoxifying enzyme, aldehyde dehydrogenase (ALDH2). This mitochondrial enzyme metabolizes toxic biogenic and environmental aldehydes, including the endogenously produced 4-hydroxynonenal (4HNE) and the environmental pollutant acrolein, and also bioactivates nitroglycerin. ALDH2 is best known, however, for its role in ethanol metabolism. The accumulation of acetaldehyde following the consumption of even a single alcoholic beverage leads to the Asian alcohol-induced flushing syndrome in ALDH2*2 homozygotes. The ALDH2*2 allele is semidominant, and heterozygotic individuals show a similar but less severe phenotype. We recently identified a small molecule, Alda-1, that activates wild-type ALDH2 and restores near-wild-type activity to ALDH2*2. The structures of Alda-1 bound to ALDH2 and ALDH2*2 reveal how Alda-1 activates the wild-type enzyme and how it restores the activity of ALDH2*2 by acting as a structural chaperone.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.

Macromolecule Content

Total Structure Weight: 440.57 kDa
Atom Count: 34,144
Modeled Residue Count: 3,954
Deposited Residue Count: 4,000
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H	500	Homo sapiens	Mutation(s): 2 Gene Names: ALDH2, ALDM EC: 1.2.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05091 (Homo sapiens) Explore P05091 Go to UniProtKB: P05091
PHAROS: P05091 GTEx: ENSG00000111275
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05091
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BXB Query on BXB Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CB [auth H] SDF format, chain KA [auth E] SDF format, chain PA [auth F] SDF format, chain V [auth B] SDF format, chain XA [auth G] SDF format, chain P [auth A] SDF format, chain EA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain KA [auth E] MOL2 format, chain PA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain KA [auth E] mmCIF format, chain PA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain XA [auth G] mmCIF format, chain P [auth A] mmCIF format, chain EA [auth D]	AA [auth C] CB [auth H] EA [auth D] KA [auth E] P [auth A] AA [auth C], CB [auth H], EA [auth D], KA [auth E], P [auth A], PA [auth F], V [auth B], XA [auth G]	N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide C₁₅ H₁₁ Cl₂ N O₃ NMKJFZCBCIUYHI-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CB [auth H] Focus chain EA [auth D] Focus chain KA [auth E] Focus chain P [auth A] Focus chain PA [auth F] Focus chain V [auth B] Focus chain XA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain CB [auth H] Focus chain EA [auth D] Focus chain KA [auth E] Focus chain P [auth A] Focus chain PA [auth F] Focus chain V [auth B] Focus chain XA [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain LA [auth E] SDF format, chain O [auth A] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain TA [auth G] SDF format, chain U [auth B] SDF format, chain UA [auth G] SDF format, chain WA [auth G] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain ZA [auth H] SDF format, chain VA [auth G] SDF format, chain T [auth B] SDF format, chain OA [auth F] SDF format, chain NA [auth F] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain DA [auth D] SDF format, chain CA [auth D] SDF format, chain BB [auth H] MOL2 format, chain AB [auth H] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain VA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth H] mmCIF format, chain AB [auth H] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth H] mmCIF format, chain VA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth H]	AB [auth H] BB [auth H] CA [auth D] DA [auth D] GA [auth E] AB [auth H], BB [auth H], CA [auth D], DA [auth D], GA [auth E], HA [auth E], IA [auth E], J [auth A], JA [auth E], K [auth A], L [auth A], LA [auth E], M [auth A], N [auth A], NA [auth F], O [auth A], OA [auth F], QA [auth F], R [auth B], RA [auth G], S [auth B], T [auth B], TA [auth G], U [auth B], UA [auth G], VA [auth G], WA [auth G], X [auth C], Y [auth C], Z [auth C], ZA [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain OA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain OA [auth F] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain MA [auth F] SDF format, chain Q [auth B] SDF format, chain SA [auth G] SDF format, chain YA [auth H] SDF format, chain W [auth C] SDF format, chain I [auth A] SDF format, chain FA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain MA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain YA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain MA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain YA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth E]	BA [auth D] FA [auth E] I [auth A] MA [auth F] Q [auth B] BA [auth D], FA [auth E], I [auth A], MA [auth F], Q [auth B], SA [auth G], W [auth C], YA [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain FA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain SA [auth G] Focus chain W [auth C] Focus chain YA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain FA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain SA [auth G] Focus chain W [auth C] Focus chain YA [auth H]

Binding Affinity Annotations
ID	Source	Binding Affinity
BXB	BindingDB: 3INL	EC50: 4300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.168 (Depositor), 0.135 (DCC)
R-Value Work: 0.136 (Depositor), 0.137 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.121	α = 90
b = 176.9	β = 94.57
c = 102.323	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling