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- PDB-1ldy: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND CYCLOHEXY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ldy | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND CYCLOHEXYL FORMAMIDE (CXF) | ||||||
![]() | ALCOHOL DEHYDROGENASE | ||||||
![]() | DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / FORMAMIDES | ||||||
Function / homology | ![]() alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ramaswamy, S. / Plapp, B.V. | ||||||
![]() | ![]() Title: Binding of formamides to liver alcohol dehydrogenase. Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V. #1: ![]() Title: Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V. #2: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.3 KB | Display | ![]() |
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PDB format | ![]() | 250.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 74.1 KB | Display | |
Data in CIF | ![]() | 102 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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) ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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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 |