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- PDB-6try: Crystal structure of human Aldehyde dehydrogenase 1A3 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6try
TitleCrystal structure of human Aldehyde dehydrogenase 1A3 in complex with MF13 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 / face development / thyroid hormone binding / 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 / Chem-NW8 / Retinaldehyde dehydrogenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGelardi, E.L.M. / Garavaglia, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Progress in the Field of Aldehyde Dehydrogenase Inhibitors: Novel Imidazo[1,2- a ]pyridines against the 1A Family.
Authors: Quattrini, L. / Gelardi, E.L.M. / Petrarolo, G. / Colombo, G. / Ferraris, D.M. / Picarazzi, F. / Rizzi, M. / Garavaglia, S. / La Motta, C.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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)114,3837
Polymers112,3552
Non-polymers2,0285
Water19811
1
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)228,76614
Polymers224,7094
Non-polymers4,05710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area22750 Å2
ΔGint-93 kcal/mol
Surface area59350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.296, 89.176, 159.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P47895, retinal dehydrogenase
#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-NW8 / 8-(4-chlorophenyl)-2-phenyl-imidazo[1,2-a]pyridine


Mass: 304.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H13ClN2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 0.4 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: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→47.96 Å / Num. obs: 48135 / % possible obs: 98.8 % / Redundancy: 4.6 % / Rpim(I) all: 0.061 / Rrim(I) all: 0.132 / Rsym value: 0.117 / Net I/av σ(I): 5.5 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.244.70.80.937260.4040.90.899.2
3.06-3.244.70.5161.435580.2640.5820.51699
3.24-3.474.60.2962.333490.1550.3370.29699.3
3.47-3.744.40.1763.931030.0940.2010.17698.8
3.74-4.140.1026.427320.0580.1180.10294.1
4.1-4.594.80.0778.526450.040.0880.07799.8
4.59-5.294.90.0659.723640.0330.0740.065100
5.29-6.484.80.0719.720190.0360.080.071100
6.48-9.174.60.04711.915920.0240.0530.04799.8
9.17-47.9574.20.04211.19260.0230.0490.04298.7

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FHZ
Resolution: 2.9→47.96 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.24 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2732 2455 5.1 %
Rwork0.1907 --
obs0.1947 48135 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.42 Å2 / Biso mean: 61.173 Å2 / Biso min: 21.78 Å2
Refinement stepCycle: final / Resolution: 2.9→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7408 0 138 11 7557
Biso mean--79.37 44.48 -
Num. residues----960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.960.37671500.3054251898
2.96-3.020.30651440.2727260398
3.02-3.080.3271300.2479252798
3.08-3.150.32891390.2537253097
3.15-3.230.30521510.2463250497
3.23-3.320.3631310.2393256297
3.32-3.420.29781100.2242254397
3.42-3.530.3351260.2083251996
3.53-3.650.28681460.2002251796
3.65-3.80.28531350.1968243494
3.8-3.970.27151410.1848232990
3.97-4.180.21751050.1717247294
4.18-4.440.2551570.15472628100
4.44-4.790.21051390.14512598100
4.79-5.270.25191520.17212603100
5.27-6.030.28771170.18862609100
6.03-7.590.27021680.19272579100
7.59-100.23051140.1547260599

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