3N80 | pdb_00003n80

Human mitochondrial aldehyde dehydrogenase, apo form

• PDB DOI: https://doi.org/10.2210/pdb3N80/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-27 Released: 2011-04-13 
• Deposition Author(s): Gonzalez-Segura, L., Hurley, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Conformational Selection During Catalysis: The role of Threonine 244 in ALDH2

Ho, K.-K., Gonzalez-Segura, L., Perez-Miller, S., Weiner, H., Hurley, T.D.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 439.79 kDa 
• Atom Count: 36,122 
• Modeled Residue Count: 3,953 
• Deposited Residue Count: 4,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase, mitochondrial	A, B, C, D, E, F, G, H	500	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AB [auth F], BA [auth C], BB [auth F], CA [auth C], CB [auth F], DA [auth C], DB [auth F], EA [auth C], EB [auth F], FA [auth C], FB [auth F], KA [auth D], KB [auth G], L [auth A], LA [auth D], LB [auth G], M [auth A], MA [auth D], MB [auth G], N [auth A], O [auth A], P [auth A], QA [auth E], RA [auth E], RB [auth H], S [auth B], SA [auth E], SB [auth H], T [auth B], TA [auth E], TB [auth H], U [auth B], UB [auth H], V [auth B], W [auth B], ZA [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
GAI	AA [auth C], HA [auth D], HB [auth G], I [auth A], IA [auth D], IB [auth G], J [auth A], JA [auth D], JB [auth G], K [auth A], OA [auth E], PA [auth E], PB [auth H], QB [auth H], R [auth B], VA [auth F], WA [auth F], XA [auth F], Y [auth C], YA [auth F], Z [auth C]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
MG	OB [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	GA [auth D], GB [auth G], NA [auth E], NB [auth H], Q [auth B], UA [auth F], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.662	α = 90
b = 152.291	β = 90
c = 177.282	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Gonzalez-Segura, L., Hurley, T.D.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-31
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary