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Yorodumi- PDB-1ldy: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND CYCLOHEXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ldy | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND CYCLOHEXYL FORMAMIDE (CXF) | ||||||
Components | ALCOHOL DEHYDROGENASE | ||||||
Keywords | DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / FORMAMIDES | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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 / Resolution: 2.5 Å | ||||||
Authors | Ramaswamy, S. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Binding of formamides to liver alcohol dehydrogenase. Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1997 Title: Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V. #2: Journal: J.Biol.Chem. / Year: 1982 Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I. #3: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution Authors: Eklund, H. / Samama, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #4: Journal: J.Mol.Biol. / Year: 1976 Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ldy.cif.gz | 310.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ldy.ent.gz | 250.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ldy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1ldy ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1ldy | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: COMMERCIAL PREPARATION OF ENZYME FROM HORSE LIVER. CDNA SEQUENCE M64864 Source: (natural) Equus caballus (horse) / Cellular location: CYTOPLASM / Organ: LIVER / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-CXF / #5: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47 % Description: ISOMORPHOUS STRUCTURE WAS USED NUMBER OF TOTAL REFLECTIONS : 122542 | ||||||||||||||||||||||||||||||
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Crystal grow | Method: batch dialysis / pH: 7 Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 ...Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM 3-BUTYLTHIOLANE 1-OXIDE. VERY CLOSE TO C-CENTERED ORTHORHOMBIC BUT SCALES VERY BADLY AS C222. SO THE SYMMETRY IS ACTUALLY P21, batch dialysis | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.99 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→12 Å / % possible obs: 92.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.042 / Net I/σ(I): 21.86 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 12 / Rsym value: 0.059 / % possible all: 81.8 |
Reflection | *PLUS Num. obs: 46126 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Mean I/σ(I) obs: 12.8 |
-Processing
Software |
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Refinement | Resolution: 2.5→12 Å / Cross valid method: UNTIL ANISOTROPIC REFINEMENT / σ(F): 0 Details: THE STRUCTURE WAS REFINED THROUGHOUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED ONLY WHEN FOUND IN ALL FOUR SUBUNITS. THE CYS 174 AND ITS EQUIVALENT LIE IN THE DISALLOWED REGION OF ...Details: THE STRUCTURE WAS REFINED THROUGHOUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED ONLY WHEN FOUND IN ALL FOUR SUBUNITS. THE CYS 174 AND ITS EQUIVALENT LIE IN THE DISALLOWED REGION OF RAMACHANDRAN PLOT - THIS IS TRUE IN SEVERAL STRUCTURES OF ADH REFINED WITH SEVERAL COMPLEXES AND IS A FEATURE OF THE ENZYME.
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Displacement parameters | Biso mean: 27.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→12 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |