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- PDB-2oxi: REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oxi | ||||||
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Title | REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION | ||||||
![]() | ALCOHOL DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE(NAD(A)-CHOH(D)) | ||||||
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 | ![]() | ||||||
![]() | Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. | ||||||
![]() | ![]() Title: Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution. Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Dauter, Z. / Wilson, K.S. #1: ![]() Title: Copper(II)-Substituted Horse Liver Alcohol Dehydrogenase: Structure of the Minor Species Authors: Formicka, G. / Zeppezauer, M. / Fey, F. / Huettermann, J. #2: ![]() Title: Electronic Absorption and Epr Spectroscopy of Copper Alcohol Dehydrogenase: Pink, Violet and Green Forms of a Type 1 Copper Center Analog Authors: Maret, W. / Kozlowski, H. #3: ![]() Title: Resonance Raman Spectroscopy of Blue Copper Proteins: Ligand and Coenzyme Effects in Copper(II)-Substituted Liver Alcohol Dehydrogenase Authors: Maret, W. / Shiemke, A.K. / Wheeler, W.D. / Loehr, T.M. / Sanders-Loehr, J. #4: ![]() Title: Resonance Raman Spectra of Copper(II)-Substituted Liver Alcohol Dehydrogenase: A Type 1 Copper Analogue Authors: Maret, W. / Zeppezauer, M. / Sanders-Loehr, J. / Loehr, T.M. #5: ![]() Title: An Epr Study of the Blue Copper Center in Horse Liver Alcohol Dehydrogenase Authors: Maret, W. / Zeppezauer, M. / Desideri, A. / Morpurgo, L. / Rotilio, G. #6: ![]() Title: Ligand Binding to the Blue Copper Center of Horse Liver Alcohol Dehydrogenase Authors: Maret, W. / Zeppezauer, M. / Desideri, A. / Morpurgo, L. / Rotilio, G. #7: ![]() Title: Active Site-Specific Reconstituted Copper(II) Horse Liver Alcohol Dehydrogenase: A Biological Model for Type 1 Cu and its Changes Upon Ligand Binding and Conformational Transitions Authors: Maret, W. / Dietrich, H. / Ruf, H.-H. / Zeppezauer, M. | ||||||
History |
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Remark 650 | HELIX RESIDUES GLY 181 - VAL 189 OF HELICES *HAA* AND *HAB* FORM A PI-HELIX (CLASS 3, 1.5 TURNS). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.9 KB | Display | ![]() |
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PDB format | ![]() | 129.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 547.2 KB | Display | ![]() |
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Full document | ![]() | 565 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: (0.49169, 0.12942, -0.86109), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. CORRESP. EULERIAN ANGLES (THETA1, THETA2, THETA3) 274.5813 120.1650 264.8520 CORRESP. SPHERICAL POLAR ANGLES (PSI, PHI, KAPPA) 85.7848 30.0067 180.2826 CORRESP. ROTATION ANGLE 179.7174 ABOUT AXIS -0.8636 -0.0735 0.4987 | |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 453 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 12 Å / Num. obs: 41119 / Num. measured all: 81533 / Rmerge(I) obs: 0.044 |
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Processing
Software |
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Refinement | Rfactor Rwork: 0.16 / Rfactor obs: 0.16 / Highest resolution: 2.1 Å Details: THERE IS DISCRETE DISORDER IN RESIDUES CYS A 46 CYS A 281 CYS A 282 CYS B 46 CYS B 282 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 12 Å / Num. reflection obs: 41119 / Rfactor obs: 0.161 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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