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- PDB-4h80: Crystal structure of human ALDH3A1 with its isozyme selective inh... -

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Basic information

Entry
Database: PDB / ID: 4h80
TitleCrystal structure of human ALDH3A1 with its isozyme selective inhibitor - N-[4-(4-methylsulfonyl-2-nitroanilino)phenyl]acetamide
ComponentsAldehyde dehydrogenase, dimeric NADP-preferring
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Catalyzes benzaldehyde / Rossmann fold / Dehydrogenase / NADP+ binding / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process ...aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process / endoplasmic reticulum / extracellular space / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / 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 NAD(P)-dependent / 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
Chem-04T / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHurley, T.D. / Parajuli, B.
CitationJournal: To be Published
Title: Kinetic and Structural Characterization of a Selective Inhibitor for Human ALDH3A1
Authors: Parajuli, B. / Georgiadis, T. / Fishel, M.L. / Hurley, T.D.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Sep 20, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, dimeric NADP-preferring
B: Aldehyde dehydrogenase, dimeric NADP-preferring
C: Aldehyde dehydrogenase, dimeric NADP-preferring
D: Aldehyde dehydrogenase, dimeric NADP-preferring
E: Aldehyde dehydrogenase, dimeric NADP-preferring
F: Aldehyde dehydrogenase, dimeric NADP-preferring
G: Aldehyde dehydrogenase, dimeric NADP-preferring
H: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)420,76116
Polymers417,9668
Non-polymers2,7958
Water3,945219
1
A: Aldehyde dehydrogenase, dimeric NADP-preferring
B: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1904
Polymers104,4912
Non-polymers6992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-28 kcal/mol
Surface area32520 Å2
MethodPISA
2
C: Aldehyde dehydrogenase, dimeric NADP-preferring
G: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1904
Polymers104,4912
Non-polymers6992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-29 kcal/mol
Surface area32380 Å2
MethodPISA
3
D: Aldehyde dehydrogenase, dimeric NADP-preferring
E: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1904
Polymers104,4912
Non-polymers6992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-28 kcal/mol
Surface area32320 Å2
MethodPISA
4
F: Aldehyde dehydrogenase, dimeric NADP-preferring
H: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1904
Polymers104,4912
Non-polymers6992
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-24 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.106, 95.380, 117.228
Angle α, β, γ (deg.)112.38, 91.68, 90.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 5 - 432 / Label seq-ID: 22 - 449

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
Aldehyde dehydrogenase, dimeric NADP-preferring / ALDHIII / Aldehyde dehydrogenase 3 / Aldehyde dehydrogenase family 3 member A1


Mass: 52245.738 Da / Num. of mol.: 8 / Mutation: S133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH3, ALDH3A1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-04T / N-(4-{[4-(methylsulfonyl)-2-nitrophenyl]amino}phenyl)acetamide


Mass: 349.362 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H15N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium acetate, 20 % PEG 3350, (3 microliters of 3 mg/mL of ALDH3A1 + 3 microlitres of mother liquor), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9869 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9869 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 123251 / Num. obs: 115363 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 2.2 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.25 / Rsym value: 0.067 / Net I/σ(I): 10.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4489 / % possible all: 72.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZA

3sza


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.465 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25529 5803 5 %RANDOM
Rwork0.23435 ---
obs0.23541 109547 93.39 %-
all-117300 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.888 Å2
Baniso -1Baniso -2Baniso -3
1-7.49 Å22.1 Å2-1.72 Å2
2---4.29 Å2-1.9 Å2
3----4.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27874 0 192 219 28285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02228815
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9839102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05653598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32424.4281249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.928155047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0515170
X-RAY DIFFRACTIONr_chiral_restr0.0690.24356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02121758
X-RAY DIFFRACTIONr_mcbond_it0.351.517848
X-RAY DIFFRACTIONr_mcangle_it0.685228922
X-RAY DIFFRACTIONr_scbond_it0.929310967
X-RAY DIFFRACTIONr_scangle_it1.6914.510162
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1690tight positional0.030.05
B1690tight positional0.020.05
C1690tight positional0.020.05
D1690tight positional0.020.05
E1690tight positional0.020.05
F1690tight positional0.020.05
G1690tight positional0.020.05
H1690tight positional0.020.05
A1537medium positional0.110.5
B1537medium positional0.070.5
C1537medium positional0.090.5
D1537medium positional0.080.5
E1537medium positional0.070.5
F1537medium positional0.040.5
G1537medium positional0.040.5
H1537medium positional0.040.5
A1690tight thermal0.060.5
B1690tight thermal0.050.5
C1690tight thermal0.040.5
D1690tight thermal0.050.5
E1690tight thermal0.050.5
F1690tight thermal0.040.5
G1690tight thermal0.040.5
H1690tight thermal0.050.5
A1537medium thermal0.062
B1537medium thermal0.052
C1537medium thermal0.052
D1537medium thermal0.062
E1537medium thermal0.052
F1537medium thermal0.042
G1537medium thermal0.042
H1537medium thermal0.052
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 318 -
Rwork0.334 6214 -
obs--71.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26280.0167-0.07542.88040.35852.94660.034-0.19740.0794-0.42690.0862-0.0644-0.34860.2015-0.12020.1-0.06730.04980.2543-0.10660.184617.7498-2.2238-43.149
20.4814-0.172-0.083.31030.74422.2514-0.0885-0.279-0.04050.50460.1609-0.06890.81210.3001-0.07230.32530.0934-0.00810.40640.01510.168118.9782-30.6816-28.7842
30.8547-0.2088-0.27362.6642-0.94573.93340.03910.1171-0.2021-0.3454-0.04080.29150.7714-0.32030.00170.1798-0.0863-0.01120.2133-0.03240.288261.1363-55.3418.5173
40.7688-0.60660.40741.4885-0.47291.25220.19710.29360.0308-0.2257-0.234-0.11830.33830.41970.03680.13030.13020.02360.36860.00710.167320.4827-22.4418-97.8805
50.3854-0.40070.25781.6566-0.12491.15950.23590.1854-0.1458-0.2149-0.10110.0620.57430.1521-0.13480.38260.118-0.09930.273-0.09080.248620.5798-50.913-83.5681
61.133-0.14590.44972.5538-0.40452.30340.03640.07380.255-0.1267-0.1735-0.2124-1.0473-0.02580.13710.57240.01990.02240.19840.05390.278860.6258-58.9501-59.6295
70.9685-0.5497-0.01673.2021-0.78922.63340.15130.25280.1668-0.2389-0.11610.1366-0.4632-0.0228-0.03520.23470.0110.0340.29650.06530.226564.4162-27.3656-6.0768
80.9434-0.44660.29223.2162-0.23591.93750.0515-0.112-0.06340.3339-0.0795-0.1754-0.2609-0.00640.02790.0918-0.0672-0.05390.23130.06770.248564.7772-86.6794-44.6899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 446
2X-RAY DIFFRACTION2B1 - 446
3X-RAY DIFFRACTION3C1 - 447
4X-RAY DIFFRACTION4D1 - 446
5X-RAY DIFFRACTION5E1 - 446
6X-RAY DIFFRACTION6F1 - 446
7X-RAY DIFFRACTION7G1 - 446
8X-RAY DIFFRACTION8H1 - 447

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