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- PDB-7adh: THREE-DIMENSIONAL STRUCTURE OF ISONICOTINIMIDYLATED LIVER ALCOHOL... -

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Entry
Database: PDB / ID: 7adh
TitleTHREE-DIMENSIONAL STRUCTURE OF ISONICOTINIMIDYLATED LIVER ALCOHOL DEHYDROGENASE
ComponentsISONICOTINIMIDYLATED 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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
ISONICOTINAMIDINE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsPlapp, B. / Eklund, H.
Citation
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.
#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: 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.
#5: 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.
#6: Journal: Biochemistry / Year: 1982
Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogeanse. 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 Dehydrogeanse. 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.
#7: 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.
#8: 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.
#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.Biol.Chem. / Year: 1979
Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Branden, C.-I.
#11: 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.
#12: Journal: J.Mol.Biol. / Year: 1978
Title: Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates
Authors: Plapp, B.V. / Eklund, H. / Branden, C.-I.
#13: Journal: J.Mol.Biol. / Year: 1978
Title: Crystallization of Liver Alcohol Denydrogenase Activated by the Modification of Amino Groups
Authors: Plapp, B.V. / Zeppezauer, E. / Branden, C.-I.
#14: Journal: J.Biol.Chem. / Year: 1978
Title: Subunit Conformation of Yeast Alcohol Dehydrogenase
Authors: Jornvall, H. / Eklund, H. / Branden, C.-I.
#15: 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.
#16: 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.
#17: 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.
#18: Journal: J.Mol.Biol. / Year: 1976
Title: Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases
Authors: Eklund, H. / Branden, C.-I. / Jornvall, H.
#19: 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.
#20: Journal: The Enzymes,Third Edition / Year: 1975
Title: Alcohol Dehydrogenases
Authors: Branden, C.-I. / Jornvall, H. / Eklund, H. / Furugren, B.
#21: 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.
#22: 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.
#23: 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.
#24: 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.
#25: 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.
#26: Journal: Arch.Biochem.Biophys. / Year: 1965
Title: Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes
Authors: Branden, C.-I.
#27: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionJan 16, 1984Processing site: BNL
Revision 1.0Jul 18, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: ISONICOTINIMIDYLATED LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,77026
Polymers39,8531
Non-polymers2,91725
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.800, 61.200, 56.500
Angle α, β, γ (deg.)90.00, 104.00, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUE 62 IS A CIS-PROLINE.
2: THIS ATOM WAS NOT LOCATED IN THE ELECTRON DENSITY MAP. COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
3: SEE REMARK 5. / 4: SEE FTNOTE 2 AND REMARK 5.

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Components

#1: Protein ISONICOTINIMIDYLATED 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: Chemical...
ChemComp-NTN / ISONICOTINAMIDINE


Mass: 121.140 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C6H7N3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 8.3 / Method: microdialysis
Details: first dialysised against R1 solution and then against R2 solution.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1buttom
20.5 MTris-HCl1buttom
30.05 MTris-HCl1reservoir1
420 %MPD1reservoir2

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Data collection

Reflection
*PLUS
Highest resolution: 3.2 Å / Num. obs: 10091

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementRfactor obs: 0.29 / Highest resolution: 3.2 Å
Details: IN THIS STRUCTURE MOST OF THE LYSINE RESIDUES WERE AMIDINATED WITH METHYL ISONICOTINIMIDATE. THE DETERMINATION OF WHICH LYSINE RESIDUES WERE MODIFIED AND THEIR SEPARATION INTO CLASSES WAS ...Details: IN THIS STRUCTURE MOST OF THE LYSINE RESIDUES WERE AMIDINATED WITH METHYL ISONICOTINIMIDATE. THE DETERMINATION OF WHICH LYSINE RESIDUES WERE MODIFIED AND THEIR SEPARATION INTO CLASSES WAS BASED ON THE ELECTRON DENSITY MAP. THE FOLLOWING LYSINES WERE MODIFIED - 10, 18, 19, 39, 88, 99, 113, 135, 159, 168, 185, 188, 212, 228, 231, 247, 325, 330, 354. THE FOLLOWING LYSINES WERE PROBABLY MODIFIED - 5, 8, 32, 226. THE FOLLOWING LYSINES WERE NOT MODIFIED OR UNCERTAIN - 104, 223, 248, 315, 323, 338, 339.
Refinement stepCycle: LAST / Highest resolution: 3.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 186 0 2970
Refinement
*PLUS
Highest resolution: 3.2 Å / Rfactor obs: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS

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