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- PDB-1lde: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lde | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE | ||||||
![]() | LIVER ALCOHOL DEHYDROGENASE![]() | ||||||
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Function / homology | ![]() alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / ![]() ![]() 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. / Samma, 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 | ![]() | 300.8 KB | Display | ![]() |
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PDB format | ![]() | 242.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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-FPI / ![]() #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 | ||||||||||||||||||||||||||||||
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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: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→20 Å / Num. obs: 94632 / % possible obs: 88.8 % / Redundancy: 2.1 % / Rsym value: 0.035 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 8.8 / Rsym value: 0.087 / % possible all: 77.2 |
Reflection | *PLUS Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.087 |
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Processing
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Refinement | Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE STRUCTURE WAS REFINED THROUG OUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED AUTOMATICALLY BY THE PROGRAM ARP.
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Displacement parameters | Biso mean: 18.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'REFMAC' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |