3N80

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175
R-Value Work: 0.149
R-Value Observed: 0.151

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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): 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05091
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth G] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain TB [auth H] SDF format, chain U [auth B] SDF format, chain UB [auth H] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth H] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth H] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain RB [auth H] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth H] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth H] mmCIF format, chain U [auth B] mmCIF format, chain UB [auth H] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain ZA [auth F]	AB [auth F] BA [auth C] BB [auth F] CA [auth C] CB [auth F] 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		Interactions Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain S [auth B] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UB [auth H] Focus chain V [auth B] Focus chain W [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain EB [auth F] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain S [auth B] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UB [auth H] Focus chain V [auth B] Focus chain W [auth B] Focus chain ZA [auth F]
GAI Query on GAI Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain HB [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain IB [auth G] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain JB [auth G] SDF format, chain K [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain PB [auth H] SDF format, chain QB [auth H] SDF format, chain R [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain PB [auth H] MOL2 format, chain QB [auth H] MOL2 format, chain R [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth G] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth G] mmCIF format, chain K [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain PB [auth H] mmCIF format, chain QB [auth H] mmCIF format, chain R [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth C]	AA [auth C] HA [auth D] HB [auth G] I [auth A] IA [auth D] 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		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain QB [auth H] Focus chain R [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain QB [auth H] Focus chain R [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain OB [auth H] MOL2 format, chain OB [auth H] mmCIF format, chain OB [auth H]	OB [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain OB [auth H] Interactions & Density Focus chain OB [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain GB [auth G] SDF format, chain NA [auth E] SDF format, chain NB [auth H] SDF format, chain Q [auth B] SDF format, chain UA [auth F] SDF format, chain X [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain NA [auth E] MOL2 format, chain NB [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain X [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth G] mmCIF format, chain NA [auth E] mmCIF format, chain NB [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain X [auth C]	GA [auth D] GB [auth G] NA [auth E] NB [auth H] Q [auth B] 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		Interactions Focus chain GA [auth D] Focus chain GB [auth G] Focus chain NA [auth E] Focus chain NB [auth H] Focus chain Q [auth B] Focus chain UA [auth F] Focus chain X [auth C] Interactions & Density Focus chain GA [auth D] Focus chain GB [auth G] Focus chain NA [auth E] Focus chain NB [auth H] Focus chain Q [auth B] Focus chain UA [auth F] Focus chain X [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B, C, D, E 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
R-Value Work: 0.149
R-Value Observed: 0.151
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Gonzalez-Segura, L.

Hurley, T.D.

Revision History (Full details and data files)

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