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- PDB-2vle: The structure of daidzin, a naturally occurring anti alcohol- add... -

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Basic information

Entry
Database: PDB / ID: 2vle
TitleThe structure of daidzin, a naturally occurring anti alcohol- addiction agent, in complex with human mitochondrial aldehyde dehydrogenase
ComponentsALDEHYDE DEHYDROGENASE, MITOCHONDRIAL
KeywordsOXIDOREDUCTASE / TRANSIT PEPTIDE / ALDEHYDE DEHYDROGENASE / NAD / DAIDZIN / ACETYLATION / POLYMORPHISM / MITOCHONDRION / ALCOHOL ABUSE
Function / homology
Function and homology information


Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / 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 / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DAIDZIN / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLowe, E.D. / Gao, G.Y. / Johnson, L.N. / Keung, W.M.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Structure of Daidzin, a Naturally Occurring Anti-Alcohol-Addiction Agent, in Complex with Human Mitochondrial Aldehyde Dehydrogenase.
Authors: Lowe, E.D. / Gao, G.Y. / Johnson, L.N. / Keung, W.M.
History
DepositionJan 13, 2008Deposition site: PDBE / Processing site: PDBE
SupersessionAug 19, 2008ID: 1OF7
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)435,09216
Polymers431,7618
Non-polymers3,3318
Water23,8341323
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)217,5468
Polymers215,8804
Non-polymers1,6664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24620 Å2
ΔGint-124.8 kcal/mol
Surface area72800 Å2
MethodPQS
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)217,5468
Polymers215,8804
Non-polymers1,6664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23080 Å2
ΔGint-93.4 kcal/mol
Surface area72900 Å2
MethodPQS
Unit cell
Length a, b, c (Å)142.770, 150.990, 176.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998571, 0.035984, -0.039511), (0.047909, 0.275168, -0.960202), (-0.023679, -0.960722, -0.276499)141.161, 79.2145, 111.31
2given(0.263262, 0.547633, 0.79422), (0.555642, -0.759074, 0.339217), (0.788641, 0.352001, -0.504123)-15.0569, -5.64536, 28.1141
3given(-0.2665, -0.59558, -0.757801), (-0.589551, -0.521271, 0.617014), (-0.762501, 0.611196, -0.212206)154.559, 49.6882, 110.318
4given(-0.996816, -0.069768, 0.038602), (0.056627, -0.278595, 0.958738), (-0.056135, 0.957871, 0.281659)144.376, -49.6899, -79.4863
5given(0.999591, 0.028562, 0.001658), (0.028565, -0.999591, -0.001644), (0.00161, 0.001691, -0.999997)-4.31891, 147.911, 176.785
6given(-0.286901, 0.583111, 0.760045), (-0.605214, 0.504675, -0.615645), (-0.742566, -0.636619, 0.208115)-65.9575, 84.2767, 166.891
7given(0.286122, -0.537562, -0.793197), (0.530081, 0.778397, -0.336321), (0.798216, -0.324229, 0.507668)204.454, -60.4705, -13.4409

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Components

#1: Protein
ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL / ALDH CLASS 2 / ALDHI / ALDH-E2


Mass: 53970.090 Da / Num. of mol.: 8 / Fragment: RESIDUES 24-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-DZN / DAIDZIN / 4',7-DIHYDROXYISOFLAVONE / 7-O-B-D-GLUCOPYRANOSIDE


Mass: 416.378 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H20O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1323 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDAIDZIN (DZN): DAIDZIN - 7-O-GLUCOSYL-4'-HYDROXYISOFLAVONE - IS A NATURALLY OCCURRING ISOFLAVONE ...DAIDZIN (DZN): DAIDZIN - 7-O-GLUCOSYL-4'-HYDROXYISOFLAVONE - IS A NATURALLY OCCURRING ISOFLAVONE EXTRACTED FROM THE KUDZU VINE

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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: 44.9 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM MES PH 6.5, 100 MM GUANIDINE-HCL, 3 MM DITHIOTHREITOL, 5% DMSO (V/V), 10% PEG 6000 (W/V) AND 2MM DAIDZIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: May 3, 2002 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→26.6 Å / Num. obs: 143547 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.7 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CW3

1cw3


Resolution: 2.4→26.4 Å / Stereochemistry target values: ML
Details: TLS REFINEMENT WAS USED. EACH POLYPEPTIDE CHAIN WAS ASSIGNED TO A SEPARATE TLS GROUP WHEN REFINING TLS, THE OUTPUT PDB FILE ALWAYS HAS THE ANISOU RECORDS FOR THE ATOMS INVOLVED IN TLS GROUPS. ...Details: TLS REFINEMENT WAS USED. EACH POLYPEPTIDE CHAIN WAS ASSIGNED TO A SEPARATE TLS GROUP WHEN REFINING TLS, THE OUTPUT PDB FILE ALWAYS HAS THE ANISOU RECORDS FOR THE ATOMS INVOLVED IN TLS GROUPS. THE ANISOTROPIC B-FACTOR IN ANISOU RECORDS IS THE TOTAL B-FACTOR (B_TLS + B_ INDIVIDUAL). THE ISOTROPIC EQUIVALENT B-FACTOR IN ATOM RECORDS IS THE MEAN OF THE TRACE OF THE ANISOU MATRIX DIVIDED BY 10000 AND MULTIPLIED BY 8*PI2 AND REPRESENTS THE ISOTROPIC EQUIVALENT OF THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). TO OBTAIN THE INDIVIDUAL B-FACTORS, ONE NEEDS TO COMPUTE THE TLS COMPONENT (B_TLS) USING THE TLS RECORDS IN THE PDB FILE HEADER AND THEN SUBTRACT IT FROM THE TOTAL B-FACTORS (ON THE ANISOU RECORDS).
RfactorNum. reflection% reflection
Rfree0.2495 7197 5 %
Rwork0.1962 --
obs-143428 96.3 %
Refinement stepCycle: LAST / Resolution: 2.4→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30376 0 240 1323 31939
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)
10.037-0.00920.0140.0965-0.01630.1435-0.00410.03590.04070.0251-0.1109-0.0538-0.05040.091-0.0601-0.0045-0.0294-0.02060.11930.04510.099888.022215.289574.9771
20.0104-0.0243-0.00070.0544-0.05340.055-0.03370.05650.00630.0241-0.03150.05090.0113-0.1116-0.0150.0297-0.05450.02850.1988-0.06630.148250.865815.416673.5288
30.13550.0355-0.0571-0.0255-0.05220.22520.0204-0.0250.11670.0173-0.03180.0005-0.25270.03950.00580.1659-0.0782-0.0422-0.0574-0.00660.092475.736757.063265.3342
4-0.00690.0429-0.02280.02520.03320.2637-0.02220.01980.0076-0.0308-0.04720.0009-0.1532-0.11130.00310.05990.0457-0.03740.09320.00070.047764.963135.972736.6925
50.01470.0061-0.00290.0339-0.02630.076-0.0515-0.035-0.00710.14540.030.07050.0035-0.1007-0.00040.14140.05350.01160.0949-0.00830.11951.1914133.7876103.6235
60.0519-0.03670.01450.14890.04410.1441-0.01270.0005-0.01110.0891-0.053-0.0510.05670.0755-0.11090.11640.0558-0.04660.07680.03350.059788.3488135.0407102.1738
70.0361-0.03570.03420.0424-0.05160.0453-0.0654-0.0678-0.0290.09440.05590.0324-0.0382-0.0244-0.07140.28840.09320.04170.06370.03320.026365.8351113.4897140.3716
80.0734-0.08670.01320.0603-0.04420.0380.0023-0.0067-0.0545-0.0360.00070.01210.20470.06580.01340.33170.17450.0024-0.15960.00250.005777.419992.8939111.7621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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