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- PDB-4kwg: Crystal Structure Analysis of ALDH2+ALDiB13 -

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Basic information

Entry
Database: PDB / ID: 4kwg
TitleCrystal Structure Analysis of ALDH2+ALDiB13
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE/Inhibitor / ALDH2+B13 / ketone binding / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / 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 / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-bromo-5-methyl-1H-indole-2,3-dione / GUANIDINE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsHurley, T.D. / Kimble-Hill, A.C.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Development of selective inhibitors for aldehyde dehydrogenases based on substituted indole-2,3-diones.
Authors: Kimble-Hill, A.C. / Parajuli, B. / Chen, C.H. / Mochly-Rosen, D. / Hurley, T.D.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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, 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)433,33533
Polymers431,7618
Non-polymers1,57425
Water20,9331162
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)216,69717
Polymers215,8804
Non-polymers81713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23690 Å2
ΔGint-97 kcal/mol
Surface area58170 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)216,63816
Polymers215,8804
Non-polymers75712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23270 Å2
ΔGint-103 kcal/mol
Surface area58240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.506, 176.193, 101.546
Angle α, β, γ (deg.)90.000, 94.920, 90.000
Int Tables number4
Space group name H-MP1211

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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: 53970.090 Da / Num. of mol.: 8 / Fragment: UNP residues 24-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / 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, 1187 molecules

#2: Chemical ChemComp-2AK / 7-bromo-5-methyl-1H-indole-2,3-dione


Mass: 240.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6BrNO2
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH5N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 300 K / Method: sitting drop / pH: 6.4
Details: 100 mM ACES, 100 mm guanidine-HCl, 10 mm MgCl2, and 14-19% PEG 6000, pH 6.4, sitting drop, temperature 300K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorDetector: 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→50 Å / Num. obs: 226469 / % possible obs: 94.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Χ2: 1.06 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.30.157102961.148185.9
2.03-2.073.40.166103891.211186.7
2.07-2.113.40.143103911.154187.2
2.11-2.153.40.122105061.09187.9
2.15-2.23.40.112106411.074188.9
2.2-2.253.40.113107211.119189.8
2.25-2.313.40.098109171.116191.1
2.31-2.373.40.089111121.12193
2.37-2.443.40.086112301.048194.4
2.44-2.523.40.081115111.007196.3
2.52-2.613.40.076116781.006197.1
2.61-2.713.50.078117011.004198.3
2.71-2.843.60.068118470.935198.7
2.84-2.993.70.064119211.017199.1
2.99-3.173.80.061118631.001199.2
3.17-3.423.80.059118941.01199.4
3.42-3.763.80.057119401.002199.4
3.76-4.313.70.047119071.105199.5
4.31-5.433.70.038119901.061199.5
5.43-503.80.031120141.07198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMAC5.7.0029phasing
RefinementResolution: 2.1→40.39 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.779 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 10031 5.1 %RANDOM
Rwork0.1925 193565 --
obs0.1944 203938 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.93 Å2 / Biso mean: 21.7836 Å2 / Biso min: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30384 0 94 1162 31640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01931129
X-RAY DIFFRACTIONr_bond_other_d0.0010.0229519
X-RAY DIFFRACTIONr_angle_refined_deg0.9691.95242231
X-RAY DIFFRACTIONr_angle_other_deg0.686367833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58353944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39624.6291400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.164155040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.70715160
X-RAY DIFFRACTIONr_chiral_restr0.0540.24632
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02135962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027229
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 726 -
Rwork0.196 13616 -
all-14342 -
obs--94.34 %

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