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Yorodumi- PDB-2vle: The structure of daidzin, a naturally occurring anti alcohol- add... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vle | |||||||||
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Title | The structure of daidzin, a naturally occurring anti alcohol- addiction agent, in complex with human mitochondrial aldehyde dehydrogenase | |||||||||
Components | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL | |||||||||
Keywords | OXIDOREDUCTASE / TRANSIT PEPTIDE / ALDEHYDE DEHYDROGENASE / NAD / DAIDZIN / ACETYLATION / POLYMORPHISM / MITOCHONDRION / ALCOHOL ABUSE | |||||||||
Function / homology | Function and homology information Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / 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 / NAD binding / electron transfer activity / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / extracellular exosome Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Lowe, E.D. / Gao, G.Y. / Johnson, L.N. / Keung, W.M. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vle.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2vle.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2vle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vle ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vle | HTTPS FTP |
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-Related structure data
Related structure data | 1cw3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 / #3: Water | ChemComp-HOH / | Nonpolymer details | DAIDZIN (DZN): DAIDZIN - 7-O-GLUCOSYL-4'-HYDROXYISOFLAVONE - IS A NATURALLY OCCURRING ISOFLAVONE ...DAIDZIN (DZN): DAIDZIN - 7-O-GLUCOSYL-4'-HYDROXYISO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.9 % / Description: NONE |
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Crystal grow | pH: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 3, 2002 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.4→2.46 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.7 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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).
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Refinement step | Cycle: LAST / Resolution: 2.4→26.4 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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