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- PDB-7a6q: Crystal structure of human aldehyde dehydrogenase 1A3 in complex ... -

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Basic information

Entry
Database: PDB / ID: 7a6q
TitleCrystal structure of human aldehyde dehydrogenase 1A3 in complex with selective NR6 inhibitor compound
ComponentsAldehyde dehydrogenase family 1 member A3
KeywordsOXIDOREDUCTASE / Dehydrogenase isoenzyme ALDH1A3 Selective Inhibitor High grade Glioma
Function / homology
Function and homology information


nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway ...nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway / righting reflex / retinal metabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / retinol metabolic process / inner ear morphogenesis / thyroid hormone binding / face development / neuromuscular process controlling balance / NAD+ binding / locomotory behavior / protein homotetramerization / positive regulation of apoptotic process / apoptotic process / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (3-oxidanylidene-3-sodiooxy-propanoyl)oxysodium / Chem-R2Q / Retinaldehyde dehydrogenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGelardi, E.L.M. / Garavaglia, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Cancers (Basel) / Year: 2021
Title: A Selective Competitive Inhibitor of Aldehyde Dehydrogenase 1A3 Hinders Cancer Cell Growth, Invasiveness and Stemness In Vitro.
Authors: Gelardi, E.L.M. / Colombo, G. / Picarazzi, F. / Ferraris, D.M. / Mangione, A. / Petrarolo, G. / Aronica, E. / Rizzi, M. / Mori, M. / La Motta, C. / Garavaglia, S.
History
DepositionAug 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,15718
Polymers112,3552
Non-polymers2,80216
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-71 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.162, 89.509, 158.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 19 through 507 or resid 601...
21(chain B and (resid 19 through 507 or resid 601...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 19 through 507 or resid 601...A19 - 507
121(chain A and (resid 19 through 507 or resid 601...A601 - 701
131(chain A and (resid 19 through 507 or resid 601...A901
141(chain A and (resid 19 through 507 or resid 601...A1101 - 1201
211(chain B and (resid 19 through 507 or resid 601...B19 - 507
221(chain B and (resid 19 through 507 or resid 601...B601 - 701
231(chain B and (resid 19 through 507 or resid 601...B901
241(chain B and (resid 19 through 507 or resid 601...B1101 - 1201

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde dehydrogenase family 1 member A3 / Aldehyde dehydrogenase 6 / Retinaldehyde dehydrogenase 3 / RalDH3


Mass: 56177.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A3, ALDH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P47895, retinal dehydrogenase

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Non-polymers , 6 types, 54 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-R2Q / 3-(2-phenylimidazo[1,2-a]pyridin-6-yl)benzenecarbonitrile


Mass: 295.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H13N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-R2K / (3-oxidanylidene-3-sodiooxy-propanoyl)oxysodium / Disodium malonate


Mass: 148.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2Na2O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.956 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.95→48.32 Å / Num. obs: 25558 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rpim(I) all: 0.058 / Rrim(I) all: 0.121 / Rsym value: 0.105 / Net I/av σ(I): 6.7 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.95-3.114.40.78311603936600.4120.8890.7831.899.8
3.11-3.34.20.4981.51449834860.2720.570.4982.999.7
3.3-3.534.30.2982.51407432700.1630.3410.2984.899.8
3.53-3.814.40.18141349230610.0980.2070.1817.799.6
3.81-4.174.30.1086.61221028400.0590.1230.10812.199.9
4.17-4.664.10.06710.21068525810.0380.0780.06717.3100
4.66-5.394.40.06111.21005222880.0330.070.06118.299.8
5.39-6.64.10.06610.6786119360.0370.0760.06615.999.5
6.6-9.334.20.03817.3656815590.0210.0430.03823.599.9
9.33-48.3183.90.0272234148770.0150.0310.0272997.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.18.1_3865refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FHZ

5fhz


Resolution: 2.95→48.32 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 1305 5.11 %
Rwork0.1941 24214 -
obs0.1971 25519 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179 Å2 / Biso mean: 70 Å2 / Biso min: 31.09 Å2
Refinement stepCycle: final / Resolution: 2.95→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7560 0 273 38 7871
Biso mean--98.66 57.28 -
Num. residues----978
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4703X-RAY DIFFRACTION8.361TORSIONAL
12B4703X-RAY DIFFRACTION8.361TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.070.34891320.272826512783100
3.07-3.210.2971320.231326752807100
3.21-3.380.2921450.21362636278199
3.38-3.590.25451400.199326782818100
3.59-3.870.26741450.17826432788100
3.87-4.250.24311400.170827002840100
4.25-4.870.22451710.16626782849100
4.87-6.130.24821430.20322719286299
6.13-48.320.23081570.2062834299199

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