2OHX

REFINED CRYSTAL STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE-NADH COMPLEX AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 A resolution.

Al-Karadaghi, S.Cedergren-Zeppezauer, E.S.Hovmoller, S.

(1994) Acta Crystallogr.,Sect.D 50: 793-807

  • DOI: 10.1107/S0907444994005263
  • Also Cited By: 1HEU, 1HET, 1HF3

  • PubMed Abstract: 
  • The crystal structure of the ternary complex of horse liver alcohol dehydrogenase (LADH) with the coenzyme NADH and inhibitor dimethyl sulfoxide (DMSO) has been refined by simulated annealing with molecular dynamics and restrained positional refineme ...

    The crystal structure of the ternary complex of horse liver alcohol dehydrogenase (LADH) with the coenzyme NADH and inhibitor dimethyl sulfoxide (DMSO) has been refined by simulated annealing with molecular dynamics and restrained positional refinement using the program X-PLOR. The two subunits of the enzyme were refined independently. The space group was P1 with cell dimensions a = 51.8, b = 44.5, c = 94.6 A, alpha = 104.8, beta = 102.3 and gamma = 70.6 degrees. The resulting crystallographic R factor is 17.3% for 62 440 unique reflections in the resolution range 10.0-1.8 A. A total of 472 ordered solvent molecules were localized in the structure. An analysis of secondary-structure elements, solvent content and NADH binding is presented.


    Related Citations: 
    • Structural and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases
      Ohlsson, I.,Nordstrom, B.,Branden, C.-I.
      (1974) J.Mol.Biol. 89: 339
    • Structure of Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution
      Eklund, H.,Samama, J.-P.,Wallen, L.,Branden, C.-I.,Akeson, A.,Jones, T.A.
      (1981) J.Mol.Biol. 146: 561
    • Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
      Schneider, G.,Eklund, H.,Cedergren-Zeppezauer, E.,Zeppezauer, M.
      (1983) Proc.Natl.Acad.Sci.USA 80: 5289
    • Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
      Plapp, B.V.,Eklund, H.,Branden, C.-I.
      (1978) J.Mol.Biol. 122: 23
    • Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
      Cedergren-Zeppezauer, E.
      (1983) Biochemistry 22: 5761
    • Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
      Eklund, H.,Branden, C.-I.,Jornvall, H.
      (1976) J.Mol.Biol. 102: 61
    • Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase
      Plapp, B.V.,Eklund, H.,Jones, T.A.,Branden, C.-I.
      (1983) J.Biol.Chem. 258: 5537
    • X-Ray Studies of the Binding of Cibacron Blue F3Ga to Liver Alcohol Dehydrogenase
      Biellmann, J.-F.,Samama, J.-P.,Branden, C.I.,Eklund, H.
      (1979) Eur.J.Biochem. 102: 107
    • Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode
      Colonna-Cesari, F.,Perahia, D.,Karplus, M.,Eklund, H.,Branden, C.I.,Tapia, O.
      (1986) J.Biol.Chem. 261: 15273
    • Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.-P.,Jones, T.A.
      (1984) Biochemistry 23: 5982
    • X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase
      Boiwe, T.,Branden, C.-I.
      (1977) Eur.J.Biochem. 77: 173
    • Alcohol Dehydrogenases
      Branden, C.-I.,Jornvall, H.,Eklund, H.,Furugren, B.
      (1975) The Enzymes,Third Edition 11: 103
    • 5-Methylnicotinamide-Adenine Dinucleotide. Kinetic Investigation with Major and Minor Isoenzymes of Liver Alcohol Dehydrogenase and Structural Determination of its Binary Complex with Alcohol Dehydrogenase
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      (1981) Eur.J.Biochem. 118: 479
    • Structure of Liver Alcohol Dehydrogenase at 2.9-Angstroms Resolution
      Branden, C.-I.,Eklund, H.,Nordstrom, B.,Boiwe, T.,Soderlund, G.,Zeppezauer, E.,Ohlsson, I.,Akeson, A.
      (1973) Proc.Natl.Acad.Sci.USA 70: 2439
    • Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Branden, C.-I.
      (1979) J.Biol.Chem. 254: 3458
    • Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
      Eklund, H.,Samama, J.-P.,Wallen, L.
      (1982) Biochemistry 21: 4858
    • Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme
      Cedergren-Zeppezauer, E.,Samama, J.-P.,Eklund, H.
      (1982) Biochemistry 21: 4895
    • Crystallization of Liver Alcohol Dehydrogenase Activated by the Modification of Amino Groups
      Plapp, B.V.,Zeppezauer, E.,Branden, C.-I.
      (1978) J.Mol.Biol. 119: 451
    • Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution
      Eklund, H.,Nordstrom, B.,Zeppezauer, E.,Soderlund, G.,Ohlsson, I.,Boiwe, T.,Soderberg, B.-O.,Tapia, O.,Branden, C.-I.,Akeson, A.
      (1976) J.Mol.Biol. 102: 27
    • The Binding of Nucleotides to Horse Liver Alcohol Dehydrogenase
      Nordstrom, B.,Branden, C.-I.
      (1975) STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN --: 387
    • Subunit Conformation of Yeast Alcohol Dehydrogenase
      Jornvall, H.,Eklund, H.,Branden, C.-I.
      (1978) J.Biol.Chem. 253: 8414
    • The Structure of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Nordstrom, B.,Zeppezauer, E.,Soderlund, G.,Ohlsson, I.,Boiwe, T.,Branden, C.-I.
      (1974) FEBS Lett. 44: 200
    • The Conformation of Adenosine Diphosphoribose and 8-Bromoadenosine Diphosphoribose When Bound to Liver Alcohol Dehydrogenase
      Abdallah, M.A.,Biellmann, J.-F.,Nordstrom, B.,Branden, C.-I.
      (1975) Eur.J.Biochem. 50: 475
    • The Crystal Structure of Complexes between Horse Liver Alcohol Dehydrogenase and the Coenzyme Analogues 3-Iodopyridine-Adenine Dinucleotide and Pyridine-Adenine Dinucleotide
      Samama, J.-P.,Zeppezauer, E.,Biellmann, J.-F.,Branden, C.-I.
      (1977) Eur.J.Biochem. 81: 403
    • Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes
      Branden, C.-I.
      (1965) Arch.Biochem.Biophys. 112: 215
    • Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
      Eklund, H.,Plapp, B.V.,Samama, J.-P.,Branden, C.-I.
      (1982) J.Biol.Chem. 257: 14349
    • Binding of Salicylate in the Adenosine-Binding Pocket of Dehydrogenases
      Einarsson, R.,Eklund, H.,Zeppezauer, E.,Boiwe, T.,Branden, C.-I.
      (1974) Eur.J.Biochem. 49: 41


    Organizational Affiliation

    Department of Structural Chemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASE
A, B
374Equus caballusEC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Go to UniProtKB:  P00327
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.173 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.760α = 104.80
b = 44.540β = 102.30
c = 94.610γ = 70.60
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other