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- PDB-8adh: INTERDOMAIN MOTION IN LIVER ALCOHOL DEHYDROGENASE. STRUCTURAL AND... -

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Basic information

Entry
Database: PDB / ID: 8adh
TitleINTERDOMAIN MOTION IN LIVER ALCOHOL DEHYDROGENASE. STRUCTURAL AND ENERGETIC ANALYSIS OF THE HINGE BENDING MODE
ComponentsAPO-LIVER ALCOHOL 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
Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJones, T.A. / Eklund, H.
Citation
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. / Braden, C.I. / Tapia, O.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: Journal: J.Biol.Chem. / Year: 1978
Title: Subunit Conformation of Yeast Alcohol Dehydrogenase
Authors: Jornvall, H. / Eklund, H. / Branden, C.-I.
#7: 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.
#8: 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.
#9: Journal: The Enzymes,Third Edition / Year: 1975
Title: Alcohol Dehydrogenases
Authors: Branden, C.-I. / Jornvall, H. / Eklund, H. / Furugren, B.
#10: 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.
#11: 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.
#12: 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.
#13: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionApr 20, 1989Processing site: BNL
SupersessionOct 15, 1989ID: 4ADH
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 9, 2012Group: Structure summary
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APO-LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9843
Polymers39,8531
Non-polymers1312
Water3,027168
1
A: APO-LIVER ALCOHOL DEHYDROGENASE
hetero molecules

A: APO-LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9686
Polymers79,7072
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3470 Å2
ΔGint-99 kcal/mol
Surface area28140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.000, 75.200, 181.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUE PRO 62 IS A CIS PROLINE.

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Components

#1: Protein APO-LIVER ALCOHOL DEHYDROGENASE


Mass: 39853.273 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.19 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 2 168 2955
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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