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- PDB-3hud: THE STRUCTURE OF HUMAN BETA 1 BETA 1 ALCOHOL DEHYDROGENASE: CATAL... -

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Basic information

Entry
Database: PDB / ID: 3hud
TitleTHE STRUCTURE OF HUMAN BETA 1 BETA 1 ALCOHOL DEHYDROGENASE: CATALYTIC EFFECTS OF NON-ACTIVE-SITE SUBSTITUTIONS
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / zinc ion binding / nucleoplasm ...all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / zinc ion binding / nucleoplasm / plasma membrane / 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 / All-trans-retinol dehydrogenase [NAD(+)] ADH1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsHurley, T.D. / Bosron, W.F. / Hamilton, J.A. / Amzel, L.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Structure of human beta 1 beta 1 alcohol dehydrogenase: catalytic effects of non-active-site substitutions.
Authors: Hurley, T.D. / Bosron, W.F. / Hamilton, J.A. / Amzel, L.M.
History
DepositionJan 4, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,1358
Polymers79,5472
Non-polymers1,5886
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-87 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.590, 45.050, 93.860
Angle α, β, γ (deg.)91.93, 102.50, 68.82
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 62 / 2: CIS PROLINE - PRO B 62
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0828, 0.9748, -0.207), (0.9724, -0.1244, -0.197), (-0.218, -0.185, -0.958)
Vector: -11.193, -7.282, -90.408)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein ALCOHOL DEHYDROGENASE /


Mass: 39773.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00325, 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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Nonpolymer detailsZN 375 IS THE STRUCTURAL ZINC ATOM. ZN 376 IS THE CATALYTIC ZINC ATOM. NAD 377 IS THE NAD+ MOLECULE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMsodium phosphate1reservoir
21 mMNAD+1reservoir
312.5 %(w/v)PEG80001reservoir
410-15 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.88 Å / Num. obs: 11114 / Observed criterion σ(I): 0.2 / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.2→8 Å / Rfactor Rwork: 0.179 / Rfactor obs: 0.179 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 92 0 5654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.56
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.56

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