+Open data
-Basic information
Entry | Database: PDB / ID: 7k35 | ||||||
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Title | EQADH-NADH-4-METHYLBENZYL ALCOHOL, p21 | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / NADH / horse liver | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / ethanol oxidation / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Plapp, B.V. / Ramaswamy, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2021 Title: Alternative binding modes in abortive NADH-alcohol complexes of horse liver alcohol dehydrogenase. Authors: Plapp, B.V. / Subramanian, R. #1: Journal: Biochemistry / Year: 2012 Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. #2: Journal: Biochemistry / Year: 2017 Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S. #3: Journal: Biochemistry / Year: 1994 Title: Structures of horse liver alcohol dehydrogenase complexed with NAD+ and substituted benzyl alcohols. Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k35.cif.gz | 575.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k35.ent.gz | 464 KB | Display | PDB format |
PDBx/mmJSON format | 7k35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/7k35 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/7k35 | HTTPS FTP |
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-Related structure data
Related structure data | 6xt2C 7jqaC 5vl0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 1266 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-VTG / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.25 Å3/Da / Density % sol: 45 % / Description: BLOCK |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 10 MG/ML ENZYME DIALYZED AGAINST 50 MM AMMONIUM N-[TRIS(HYDROXYLMETHYL)METHYL]2-AMINOETHANE SULFONATE (PH 6.7 AT 25 DEG C) WITH 1 MM NAD+ AND 10 MM 4-METHY-BENZYL ALCOHOL AS THE ...Details: 10 MG/ML ENZYME DIALYZED AGAINST 50 MM AMMONIUM N-[TRIS(HYDROXYLMETHYL)METHYL]2-AMINOETHANE SULFONATE (PH 6.7 AT 25 DEG C) WITH 1 MM NAD+ AND 10 MM 4-METHY-BENZYL ALCOHOL AS THE CONCENTRATION OF 2-METHYL-2,4-PENTANEDIOL WAS RAISED TO 25 %. CRYSTAL WAS MOUNTED ON A FIBER LOOP AND FLASH VITRIFIED BY PLUNGING IT INTO LIQUID N2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.96 Å / Num. obs: 456390 / % possible obs: 99.2 % / Redundancy: 9.53 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.12 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 45908 / Rrim(I) all: 0.643 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vl0 Resolution: 1.2→19.96 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.943 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.888 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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