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- PDB-2ohx: REFINED CRYSTAL STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE-NADH COM... -

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Entry
Database: PDB / ID: 2ohx
TitleREFINED CRYSTAL STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE-NADH COMPLEX AT 1.8 ANGSTROMS RESOLUTION
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsAl-Karadaghi, S. / Cedergren-Zeppezauer, E.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 A resolution.
Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Hovmoller, S.
#1: Journal: J.Biol.Chem. / Year: 1986
Title: Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode
Authors: Colonna-Cesari, F. / Perahia, D. / Karplus, M. / Eklund, H. / Branden, C.I. / Tapia, O.
#2: Journal: Biochemistry / Year: 1984
Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Samama, J.-P. / Jones, T.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
Authors: Schneider, G. / Eklund, H. / Cedergren-Zeppezauer, E. / Zeppezauer, M.
#4: Journal: J.Biol.Chem. / Year: 1983
Title: Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase
Authors: Plapp, B.V. / Eklund, H. / Jones, T.A. / Branden, C.-I.
#5: Journal: Biochemistry / Year: 1983
Title: Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
Authors: Cedergren-Zeppezauer, E.
#6: 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.
#7: Journal: Biochemistry / Year: 1982
Title: 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- ...Title: 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
Authors: Cedergren-Zeppezauer, E. / Samama, J.-P. / Eklund, H.
#8: Journal: Biochemistry / Year: 1982
Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Samama, J.-P. / Wallen, L.
#9: Journal: Eur.J.Biochem. / Year: 1981
Title: 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
Authors: Samama, J.-P. / Wrixon, A.D. / Biellmann, J.-F.
#10: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution
Authors: Eklund, H. / Samama, J.-P. / Wallen, L. / Branden, C.-I. / Akeson, A. / Jones, T.A.
#11: Journal: J.Biol.Chem. / Year: 1979
Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Branden, C.-I.
#12: Journal: Eur.J.Biochem. / Year: 1979
Title: X-Ray Studies of the Binding of Cibacron Blue F3Ga to Liver Alcohol Dehydrogenase
Authors: Biellmann, J.-F. / Samama, J.-P. / Branden, C.I. / Eklund, H.
#13: Journal: J.Mol.Biol. / Year: 1978
Title: Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
Authors: Plapp, B.V. / Eklund, H. / Branden, C.-I.
#14: Journal: J.Mol.Biol. / Year: 1978
Title: Crystallization of Liver Alcohol Dehydrogenase Activated by the Modification of Amino Groups
Authors: Plapp, B.V. / Zeppezauer, E. / Branden, C.-I.
#15: Journal: J.Biol.Chem. / Year: 1978
Title: Subunit Conformation of Yeast Alcohol Dehydrogenase
Authors: Jornvall, H. / Eklund, H. / Branden, C.-I.
#16: Journal: Eur.J.Biochem. / Year: 1977
Title: The Crystal Structure of Complexes between Horse Liver Alcohol Dehydrogenase and the Coenzyme Analogues 3-Iodopyridine-Adenine Dinucleotide and Pyridine-Adenine Dinucleotide
Authors: Samama, J.-P. / Zeppezauer, E. / Biellmann, J.-F. / Branden, C.-I.
#17: Journal: Eur.J.Biochem. / Year: 1977
Title: X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase
Authors: Boiwe, T. / Branden, C.-I.
#18: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.-O. / Tapia, O. / Branden, C.-I. / Akeson, A.
#19: Journal: J.Mol.Biol. / Year: 1976
Title: Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
Authors: Eklund, H. / Branden, C.-I. / Jornvall, H.
#20: Journal: 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
Year: 1975
Title: The Binding of Nucleotides to Horse Liver Alcohol Dehydrogenase
Authors: Nordstrom, B. / Branden, C.-I.
#21: Journal: The Enzymes,Third Edition / Year: 1975
Title: Alcohol Dehydrogenases
Authors: Branden, C.-I. / Jornvall, H. / Eklund, H. / Furugren, B.
#22: Journal: Eur.J.Biochem. / Year: 1975
Title: The Conformation of Adenosine Diphosphoribose and 8-Bromoadenosine Diphosphoribose When Bound to Liver Alcohol Dehydrogenase
Authors: Abdallah, M.A. / Biellmann, J.-F. / Nordstrom, B. / Branden, C.-I.
#23: Journal: FEBS Lett. / Year: 1974
Title: The Structure of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Branden, C.-I.
#24: Journal: J.Mol.Biol. / Year: 1974
Title: Structural and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases
Authors: Ohlsson, I. / Nordstrom, B. / Branden, C.-I.
#25: Journal: Eur.J.Biochem. / Year: 1974
Title: Binding of Salicylate in the Adenosine-Binding Pocket of Dehydrogenases
Authors: Einarsson, R. / Eklund, H. / Zeppezauer, E. / Boiwe, T. / Branden, C.-I.
#26: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Structure of Liver Alcohol Dehydrogenase at 2.9-Angstroms Resolution
Authors: Branden, C.-I. / Eklund, H. / Nordstrom, B. / Boiwe, T. / Soderlund, G. / Zeppezauer, E. / Ohlsson, I. / Akeson, A.
#27: Journal: Arch.Biochem.Biophys. / Year: 1965
Title: Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes
Authors: Branden, C.-I.
#28: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionAug 24, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX GLY 181 - VAL 189 IS A PI-HELIX (CLASS 3, 1.5 TURNS) AT HELIX IDENTIFICATION HAA AND HAB.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,45110
Polymers79,7072
Non-polymers1,7458
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-112 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.760, 44.540, 94.610
Angle α, β, γ (deg.)104.80, 102.30, 70.60
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO A 62 AND PRO B 62 ARE CIS PROLINES.
2: THE FOLLOWING RESIDUES WERE DISCRETELY DISORDERED: CYS A 281, CYS A 282, AND CYS B 282
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.12925, 0.98584, -0.10681), (0.98615, -0.13908, -0.09037), (-0.10394, -0.09366, -0.99016)
Vector: 0.399, -0.2149, 0.4423)

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Components

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 39853.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal grow
*PLUS
pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 %enzyme11
20.05 MTES12
3NADH115mg
4DMSO110.5ml
5NADH125mg
6DMSO120.5ml

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 62440 / % possible obs: 88.5 % / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→10 Å / Rfactor Rwork: 0.173 / Rfactor obs: 0.173 / σ(F): 0
Details: THE FOLLOWING RESIDUES WERE DISCRETELY DISORDERED: CYS A 281, CYS A 282, AND CYS B 282
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 100 459 6129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.91
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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