3N82 | pdb_00003n82

T244A mutant of Human mitochondrial aldehyde dehydrogenase, NADH complex

PDB DOI: https://doi.org/10.2210/pdb3N82/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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: 2.25 Å
R-Value Free:
0.219 (Depositor), 0.222 (DCC)
R-Value Work:
0.168 (Depositor), 0.171 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 443.7 kDa
Atom Count: 33,806
Modeled Residue Count: 3,952
Deposited Residue Count: 4,000
Unique protein chains: 1

Macromolecules

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| 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): 1 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain SA [auth E] SDF format, chain V [auth B] SDF format, chain QB [auth H] SDF format, chain O [auth A] SDF format, chain KB [auth G] SDF format, chain KA [auth D] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain QB [auth H] MOL2 format, chain O [auth A] MOL2 format, chain KB [auth G] MOL2 format, chain KA [auth D] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain SA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain QB [auth H] mmCIF format, chain O [auth A] mmCIF format, chain KB [auth G] mmCIF format, chain KA [auth D]	CB [auth F] DA [auth C] KA [auth D] KB [auth G] O [auth A] CB [auth F], DA [auth C], KA [auth D], KB [auth G], O [auth A], QB [auth H], SA [auth E], V [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CB [auth F] Focus chain DA [auth C] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain O [auth A] Focus chain QB [auth H] Focus chain SA [auth E] Focus chain V [auth B] Interactions & Density Focus chain CB [auth F] Focus chain DA [auth C] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain O [auth A] Focus chain QB [auth H] Focus chain SA [auth E] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain IA [auth D] SDF format, chain JB [auth G] SDF format, chain L [auth A] SDF format, chain OB [auth H] SDF format, chain PB [auth H] SDF format, chain RA [auth E] SDF format, chain ZA [auth F] SDF format, chain Z [auth C] SDF format, chain YA [auth F] SDF format, chain XA [auth F] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain QA [auth E] SDF format, chain PA [auth E] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain JA [auth D] SDF format, chain IB [auth G] SDF format, chain HB [auth G] SDF format, chain BB [auth F] SDF format, chain AB [auth F] SDF format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain L [auth A] MOL2 format, chain OB [auth H] MOL2 format, chain PB [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain ZA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain IB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain BB [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain JB [auth G] mmCIF format, chain L [auth A] mmCIF format, chain OB [auth H] mmCIF format, chain PB [auth H] mmCIF format, chain RA [auth E] mmCIF format, chain ZA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain IB [auth G] mmCIF format, chain HB [auth G] mmCIF format, chain BB [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth F] BA [auth C] BB [auth F] CA [auth C] AA [auth C], AB [auth F], BA [auth C], BB [auth F], CA [auth C], HB [auth G], IA [auth D], IB [auth G], JA [auth D], JB [auth G], L [auth A], M [auth A], N [auth A], OB [auth H], PA [auth E], PB [auth H], QA [auth E], RA [auth E], T [auth B], U [auth B], XA [auth F], YA [auth F], Z [auth C], ZA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OB [auth H] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OB [auth H] Focus chain PA [auth E] Focus chain PB [auth H] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F]
GAI Query on GAI Download:Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain OA [auth E] SDF format, chain Y [auth C] SDF format, chain WA [auth F] SDF format, chain VA [auth F] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain NB [auth H] SDF format, chain NA [auth E] SDF format, chain K [auth A] SDF format, chain HA [auth D] SDF format, chain GB [auth G] SDF format, chain GA [auth D] MOL2 format, chain FB [auth G] MOL2 format, chain OA [auth E] MOL2 format, chain Y [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain NB [auth H] MOL2 format, chain NA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth G] MOL2 format, chain GA [auth D] mmCIF format, chain FB [auth G] mmCIF format, chain OA [auth E] mmCIF format, chain Y [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain NB [auth H] mmCIF format, chain NA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth G] mmCIF format, chain GA [auth D]	FB [auth G] GA [auth D] GB [auth G] HA [auth D] K [auth A] FB [auth G], GA [auth D], GB [auth G], HA [auth D], K [auth A], NA [auth E], NB [auth H], OA [auth E], R [auth B], S [auth B], VA [auth F], WA [auth F], Y [auth C]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain FB [auth G] Focus chain GA [auth D] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain K [auth A] Focus chain NA [auth E] Focus chain NB [auth H] Focus chain OA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain FB [auth G] Focus chain GA [auth D] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain K [auth A] Focus chain NA [auth E] Focus chain NB [auth H] Focus chain OA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain Y [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain TA [auth F] SDF format, chain P [auth B] SDF format, chain LB [auth H] SDF format, chain LA [auth E] SDF format, chain I [auth A] SDF format, chain EA [auth D] SDF format, chain DB [auth G] MOL2 format, chain W [auth C] MOL2 format, chain TA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain LB [auth H] MOL2 format, chain LA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth G] mmCIF format, chain W [auth C] mmCIF format, chain TA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain LB [auth H] mmCIF format, chain LA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth G]	DB [auth G] EA [auth D] I [auth A] LA [auth E] LB [auth H] DB [auth G], EA [auth D], I [auth A], LA [auth E], LB [auth H], P [auth B], TA [auth F], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DB [auth G] Focus chain EA [auth D] Focus chain I [auth A] Focus chain LA [auth E] Focus chain LB [auth H] Focus chain P [auth B] Focus chain TA [auth F] Focus chain W [auth C] Interactions & Density Focus chain DB [auth G] Focus chain EA [auth D] Focus chain I [auth A] Focus chain LA [auth E] Focus chain LB [auth H] Focus chain P [auth B] Focus chain TA [auth F] Focus chain W [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EB [auth G] SDF format, chain MA [auth E] SDF format, chain MB [auth H] SDF format, chain X [auth C] SDF format, chain UA [auth F] SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain FA [auth D] MOL2 format, chain EB [auth G] MOL2 format, chain MA [auth E] MOL2 format, chain MB [auth H] MOL2 format, chain X [auth C] MOL2 format, chain UA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth D] mmCIF format, chain EB [auth G] mmCIF format, chain MA [auth E] mmCIF format, chain MB [auth H] mmCIF format, chain X [auth C] mmCIF format, chain UA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth D]	EB [auth G] FA [auth D] J [auth A] MA [auth E] MB [auth H] EB [auth G], FA [auth D], J [auth A], MA [auth E], MB [auth H], Q [auth B], UA [auth F], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EB [auth G] Focus chain FA [auth D] Focus chain J [auth A] Focus chain MA [auth E] Focus chain MB [auth H] Focus chain Q [auth B] Focus chain UA [auth F] Focus chain X [auth C] Interactions & Density Focus chain EB [auth G] Focus chain FA [auth D] Focus chain J [auth A] Focus chain MA [auth E] Focus chain MB [auth H] Focus chain Q [auth B] Focus chain UA [auth F] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.219 (Depositor), 0.222 (DCC)
R-Value Work: 0.168 (Depositor), 0.171 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.216	α = 90
b = 150.724	β = 90
c = 177.299	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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: 2017-11-08
Changes: Refinement description
Version 1.3: 2018-01-31
Changes: Database references
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description