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- PDB-3sz9: Crystal structure of human ALDH2 modified with the beta-eliminati... -

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Basic information

Entry
Database: PDB / ID: 3sz9
TitleCrystal structure of human ALDH2 modified with the beta-elimination product of Aldi-3; 1-(4-ethylbenzene)prop-2-en-1-one
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / ALDH / Aldi-3 / inhibitor / Rossmann Fold / Oxidoreductase / Covalent adduct / Mitochondria / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation ...Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANIDINE / 1-(4-ethylphenyl)propan-1-one / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPerez-Miller, S. / Hurley, T.D.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: Discovery of a novel class of covalent inhibitor for aldehyde dehydrogenases.
Authors: Khanna, M. / Chen, C.H. / Kimble-Hill, A. / Parajuli, B. / Perez-Miller, S. / Baskaran, S. / Kim, J. / Dria, K. / Vasiliou, V. / Mochly-Rosen, D. / Hurley, T.D.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant
Authors: Perez-Miller, S. / Younus, H. / Vanam, R. / Chen, C.-H. / Mochly-Rosen, D. / Hurley, T.D.
#2: Journal: Science / Year: 2008
Title: Activation of Aldehyde Dehydrogenase-2 Reduces Ischemic Damage to the Heart
Authors: Chen, C.-H. / Budas, G.R. / Churchill, E.N. / Disatnik, M.-H. / Hurley, T.D. / Mochly-Rosen, D.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,84563
Polymers435,9978
Non-polymers3,84855
Water46,7312594
1
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,79213
Polymers108,9992
Non-polymers79311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-24 kcal/mol
Surface area34620 Å2
MethodPISA
2
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,03717
Polymers108,9992
Non-polymers1,03815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-25 kcal/mol
Surface area34840 Å2
MethodPISA
3
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,16219
Polymers108,9992
Non-polymers1,16217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-23 kcal/mol
Surface area34670 Å2
MethodPISA
4
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,85414
Polymers108,9992
Non-polymers85512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-23 kcal/mol
Surface area34730 Å2
MethodPISA
5
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,83030
Polymers217,9994
Non-polymers1,83126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20690 Å2
ΔGint-64 kcal/mol
Surface area59500 Å2
MethodPISA
6
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,01633
Polymers217,9994
Non-polymers2,01729
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20780 Å2
ΔGint-64 kcal/mol
Surface area59440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.522, 151.052, 177.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThere are two tetramers in the asymmetric unit (chains A, B, C, & D and chains E, F, G & H)

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Aldehyde dehydrogenase, mitochondrial / ALDH class 2 / ALDH-E2 / ALDHI


Mass: 54499.629 Da / Num. of mol.: 8 / Fragment: Mature sequence, UNP residues 18-517
Source method: isolated from a genetically manipulated source
Details: lacks mitochondrial leader sequence / Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)

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Non-polymers , 5 types, 2649 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CH5N3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-I3E / 1-(4-ethylphenyl)propan-1-one / 1-(4-ethylphenyl)prop-2-en-1-one, bound form


Mass: 162.228 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H14O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2594 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE STARTING MATERIAL IS 1-(4-ETHYLPHENYL)PROP-2-EN-1-ONE. IT BINDS COVALENTLY TO CYS 302. I3E ...THE STARTING MATERIAL IS 1-(4-ETHYLPHENYL)PROP-2-EN-1-ONE. IT BINDS COVALENTLY TO CYS 302. I3E CORRESPONDS TO THE FINAL PRODUCT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.4
Details: 100 MM ACES (N-[2-ACETAMIDO]-2-AMINOETHANE SULFONIC ACID), 10MM MGCL2, 100 MM GUANIDINE HCL, 16-17% W/V PEG 6000, 4MM DTT, pH 6.4, vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9869 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9869 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 217889 / % possible obs: 99.7 % / Observed criterion σ(I): 0.2 / Redundancy: 5.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.064 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.145.40.529107750.908199.7
2.14-2.185.40.458108150.893199.9
2.18-2.225.50.408108330.919199.9
2.22-2.265.50.356108210.889199.9
2.26-2.315.50.31107910.885199.9
2.31-2.375.50.282108310.892199.9
2.37-2.425.50.255108530.882199.9
2.42-2.495.60.229107860.894199.7
2.49-2.565.60.197108550.879199.8
2.56-2.655.60.162108430.89199.9
2.65-2.745.60.157108740.903199.9
2.74-2.855.60.126108700.933199.8
2.85-2.985.60.11108850.972199.9
2.98-3.145.60.092109021.063199.9
3.14-3.335.50.083109291.317199.9
3.33-3.595.50.075109691.631100
3.59-3.955.50.065109721.8091100
3.95-4.525.40.049110031.524199.6
4.52-5.75.40.038111001.124199.8
5.7-505.60.033111821.066197.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1O05

1o05


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.077 / SU ML: 0.136 / SU R Cruickshank DPI: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 5541 2.5 %RANDOM
Rwork0.1745 ---
obs0.1759 217729 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.92 Å2 / Biso mean: 26.0324 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30393 0 260 2594 33247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02231436
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.95542595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18853945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76224.7271426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.656155102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.82515160
X-RAY DIFFRACTIONr_chiral_restr0.0870.24673
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124164
X-RAY DIFFRACTIONr_mcbond_it1.0761.519683
X-RAY DIFFRACTIONr_mcangle_it1.772231600
X-RAY DIFFRACTIONr_scbond_it3.199311753
X-RAY DIFFRACTIONr_scangle_it4.824.510995
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 385 -
Rwork0.213 15451 -
all-15836 -
obs-15451 98.88 %

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