3N83 | pdb_00003n83

T244A mutant of human mitochondrial aldehyde dehydrogenase, NAD complex

PDB DOI: https://doi.org/10.2210/pdb3N83/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: 1.90 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 441.73 kDa
Atom Count: 34,066
Modeled Residue Count: 3,952
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): 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% 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
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FB [auth G] SDF format, chain HA [auth D] SDF format, chain KB [auth H] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain T [auth B] SDF format, chain XA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain KB [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain XA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain KB [auth H] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain XA [auth F]	AA [auth C] FB [auth G] HA [auth D] KB [auth H] N [auth A] AA [auth C], FB [auth G], HA [auth D], KB [auth H], N [auth A], NA [auth E], T [auth B], XA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain FB [auth G] Focus chain HA [auth D] Focus chain KB [auth H] Focus chain N [auth A] Focus chain NA [auth E] Focus chain T [auth B] Focus chain XA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain FB [auth G] Focus chain HA [auth D] Focus chain KB [auth H] Focus chain N [auth A] Focus chain NA [auth E] Focus chain T [auth B] Focus chain XA [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain DB [auth G] SDF format, chain EB [auth G] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain IB [auth H] SDF format, chain JB [auth H] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain W [auth C] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain JB [auth H] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain DB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain IB [auth H] mmCIF format, chain JB [auth H] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	CB [auth G] DB [auth G] EB [auth G] FA [auth D] GA [auth D] CB [auth G], DB [auth G], EB [auth G], FA [auth D], GA [auth D], IB [auth H], JB [auth H], K [auth A], L [auth A], LA [auth E], M [auth A], MA [auth E], R [auth B], S [auth B], SA [auth F], TA [auth F], UA [auth F], VA [auth F], W [auth C], WA [auth F], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CB [auth G] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GAI Query on GAI Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HB [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain V [auth C] SDF format, chain ZA [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain ZA [auth G] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain ZA [auth G]	AB [auth G] BB [auth G] CA [auth D] DA [auth D] EA [auth D] AB [auth G], BB [auth G], CA [auth D], DA [auth D], EA [auth D], HB [auth H], J [auth A], JA [auth E], KA [auth E], P [auth B], PA [auth F], Q [auth B], QA [auth F], RA [auth F], V [auth C], ZA [auth G]	GUANIDINE C H₅ N₃ ZRALSGWEFCBTJO-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HB [auth H] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain V [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HB [auth H] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain V [auth C] Focus chain ZA [auth G]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GB [auth H] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain U [auth C] SDF format, chain YA [auth G] MOL2 format, chain BA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain YA [auth G] mmCIF format, chain BA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain U [auth C] mmCIF format, chain YA [auth G]	BA [auth D] GB [auth H] I [auth A] IA [auth E] O [auth B] BA [auth D], GB [auth H], I [auth A], IA [auth E], O [auth B], OA [auth F], U [auth C], YA [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GB [auth H] Focus chain I [auth A] Focus chain IA [auth E] Focus chain O [auth B] Focus chain OA [auth F] Focus chain U [auth C] Focus chain YA [auth G] Interactions & Density Focus chain BA [auth D] Focus chain GB [auth H] Focus chain I [auth A] Focus chain IA [auth E] Focus chain O [auth B] Focus chain OA [auth F] Focus chain U [auth C] Focus chain YA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.129	α = 90
b = 150.993	β = 90
c = 177.695	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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: 2014-03-12
Changes: Source and taxonomy
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2018-01-31
Changes: Database references
Version 1.5: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description