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- PDB-5l13: Structure of ALDH2 in complex with 2P3 -

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Basic information

Entry
Database: PDB / ID: 5l13
TitleStructure of ALDH2 in complex with 2P3
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / NAD binding / electron transfer activity / carbohydrate metabolic process / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6ZE / GUANIDINE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBuchman, C.D. / Hurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)R01-AA018123 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Inhibition of the Aldehyde Dehydrogenase 1/2 Family by Psoralen and Coumarin Derivatives.
Authors: Buchman, C.D. / Hurley, T.D.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)455,56552
Polymers451,5288
Non-polymers4,03644
Water30,8241711
1
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)227,72025
Polymers225,7644
Non-polymers1,95621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24820 Å2
ΔGint-96 kcal/mol
Surface area57450 Å2
MethodPISA
2
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)227,84427
Polymers225,7644
Non-polymers2,08023
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25300 Å2
ΔGint-91 kcal/mol
Surface area57430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.412, 127.049, 294.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTetramer as determined by gel filtration

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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: 56441.047 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Production host: Escherichia coli (E. coli) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)

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Non-polymers , 5 types, 1755 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH5N3
#5: Chemical
ChemComp-6ZE / 2,3,5-trimethyl-6-propyl-7H-furo[3,2-g][1]benzopyran-7-one


Mass: 270.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H18O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1711 / Source method: isolated from a natural source / Formula: H2O

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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: 42.82 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM ACES, 100 mM guanidine-HCl, 10 mM MgCl2, 4 mM dithiothreitol, 18% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 141511 / % possible obs: 94.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Net I/av σ(I): 11.239 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.444.80.28185.7
2.44-2.494.80.268186.9
2.49-2.534.80.252187.4
2.53-2.594.70.242188.2
2.59-2.644.70.218189.2
2.64-2.74.70.207190.8
2.7-2.774.70.202192.2
2.77-2.854.70.184193
2.85-2.934.70.167194
2.93-3.024.80.151195.1
3.02-3.134.80.137196.3
3.13-3.264.90.122198
3.26-3.415.10.11198.8
3.41-3.585.20.098198.1
3.58-3.815.30.087198.8
3.81-4.15.30.079197.8
4.1-4.525.20.072197.8
4.52-5.175.20.063197.6
5.17-6.515.40.054199.1
6.51-505.30.042197.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementResolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.176 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.722 / ESU R Free: 0.255
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 6966 5 %RANDOM
Rwork0.1552 ---
obs0.1578 131537 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.5 Å2 / Biso mean: 27.44 Å2 / Biso min: 6.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å2-0 Å20 Å2
2---4.89 Å20 Å2
3---3.52 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30393 0 280 1711 32384
Biso mean--36 29.36 -
Num. residues----3953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01931433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0229829
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.95842666
X-RAY DIFFRACTIONr_angle_other_deg0.745368497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09753972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73824.6391412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.894155072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.30615162
X-RAY DIFFRACTIONr_chiral_restr0.070.24648
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02136329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027361
X-RAY DIFFRACTIONr_mcbond_it1.3222.59515835
X-RAY DIFFRACTIONr_mcbond_other1.322.59515834
X-RAY DIFFRACTIONr_mcangle_it2.1233.88919787
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 509 -
Rwork0.187 8744 -
all-9253 -
obs--86.76 %

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