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Yorodumi- PDB-1hdx: THREE-DIMENSIONAL STRUCTURES OF THREE HUMAN ALCOHOL DEHYDROGENASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hdx | ||||||
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Title | THREE-DIMENSIONAL STRUCTURES OF THREE HUMAN ALCOHOL DEHYDROGENASE VARIANTS: CORRELATIONS WITH THEIR FUNCTIONAL DIFFERENCES | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(NAD(A)-CHOH(D)) | ||||||
Function / homology | Function and homology information all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / retinol metabolic process / retinoic acid metabolic process / retinoid metabolic process / zinc ion binding / nucleoplasm ...all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / retinol metabolic process / retinoic acid metabolic process / retinoid metabolic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Hurley, T.D. / Amzel, L.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Structures of three human beta alcohol dehydrogenase variants. Correlations with their functional differences. Authors: Hurley, T.D. / Bosron, W.F. / Stone, C.L. / Amzel, L.M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: The Structure of Human Beta-1 Alcohol Dehydrogenase: Catalytic Effects of Non-Active Site Substitutions Authors: Hurley, T.D. / Amzel, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hdx.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdx.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hdx_validation.pdf.gz | 997.8 KB | Display | wwPDB validaton report |
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Full document | 1hdx_full_validation.pdf.gz | 1015.2 KB | Display | |
Data in XML | 1hdx_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 1hdx_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdx ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 62 / 2: CIS PROLINE - PRO B 62 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.0786, 0.9791, -0.187), Vector: Details | THE ASYMMETRIC UNIT CONTAINS ONE DIMER OF HUMAN ALCOHOL DEHYDROGENASE. THE TRANSFORMATION PRESENTED IN *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39773.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00325, alcohol dehydrogenase |
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-Non-polymers , 5 types, 119 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.34 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.36 Å / Num. obs: 21574 / Num. measured all: 49969 / Rmerge(I) obs: 0.005 |
-Processing
Software |
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Refinement | Resolution: 2.5→7 Å / Rfactor Rwork: 0.179 / Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 7 Å / Num. reflection all: 19450 / Num. reflection obs: 19023 / σ(I): 1 / Rfactor all: 0.183 / Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.12 |