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- PDB-1agn: X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1agn
TitleX-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE
ComponentsHUMAN SIGMA ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


omega-hydroxydecanoate dehydrogenase / omega-hydroxydecanoate dehydrogenase activity / ethanol binding / aldehyde oxidase activity / all-trans-retinol dehydrogenase (NAD+) / fatty acid omega-oxidation / receptor antagonist activity / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NAD+) activity, zinc-dependent ...omega-hydroxydecanoate dehydrogenase / omega-hydroxydecanoate dehydrogenase activity / ethanol binding / aldehyde oxidase activity / all-trans-retinol dehydrogenase (NAD+) / fatty acid omega-oxidation / receptor antagonist activity / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / retinol binding / response to bacterium / response to ethanol / zinc ion binding / 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 / GroES-like superfamily / NAD(P)-binding Rossmann-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 / 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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / All-trans-retinol dehydrogenase [NAD(+)] ADH7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHurley, T.D. / Xie, P.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: X-ray structure of human class IV sigmasigma alcohol dehydrogenase. Structural basis for substrate specificity.
Authors: Xie, P. / Parsons, S.H. / Speckhard, D.C. / Bosron, W.F. / Hurley, T.D.
History
DepositionJun 4, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _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: HUMAN SIGMA ALCOHOL DEHYDROGENASE
B: HUMAN SIGMA ALCOHOL DEHYDROGENASE
C: HUMAN SIGMA ALCOHOL DEHYDROGENASE
D: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,98834
Polymers159,6974
Non-polymers4,29130
Water1629
1
A: HUMAN SIGMA ALCOHOL DEHYDROGENASE
B: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,11219
Polymers79,8492
Non-polymers2,26317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-229 kcal/mol
Surface area26240 Å2
MethodPISA
2
C: HUMAN SIGMA ALCOHOL DEHYDROGENASE
D: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,87615
Polymers79,8492
Non-polymers2,02713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-251 kcal/mol
Surface area26550 Å2
MethodPISA
3
A: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules

D: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules

B: HUMAN SIGMA ALCOHOL DEHYDROGENASE
C: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,98834
Polymers159,6974
Non-polymers4,29130
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_455x-1,y,z1
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-468 kcal/mol
Surface area58350 Å2
MethodPISA
4
B: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules

D: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules

A: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules

C: HUMAN SIGMA ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,98834
Polymers159,6974
Non-polymers4,29130
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area10420 Å2
ΔGint-466 kcal/mol
Surface area57420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.300, 94.650, 121.660
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.493966, -0.859858, -0.129006), (-0.862878, 0.466538, 0.194383), (-0.106956, 0.207334, -0.972406)26.4815, 4.1028, 84.2244
2given(-0.440698, -0.839493, 0.317862), (-0.831438, 0.248262, -0.497068), (0.338372, -0.48334, -0.807395)44.90287, 91.65095, 155.93347
3given(0.413252, 0.910136, 0.029566), (0.784111, -0.372163, 0.496653), (0.463025, -0.18206, -0.867446)-12.79606, -85.18898, 101.59405

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Components

#1: Protein
HUMAN SIGMA ALCOHOL DEHYDROGENASE / SIGMA ADH


Mass: 39924.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: THE STRUCTURE CONTAINS ONE NAD+ PER SUBUNIT / Source: (gene. exp.) Homo sapiens (human)
Description: PURCHASED FROM BOERINGER MANNHEIM (INDIANAPOLIS, IN)
Gene: HUMAN SIGMA CDNA (ADH7) / Organ: STOMACH / Plasmid: PKK223-3 / Gene (production host): HUMAN SIGMA CDNA (ADH7) / Production host: Escherichia coli (E. coli) / References: UniProt: P40394, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.06 Å3/Da / Density % sol: 59.5 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
2100 mMcacodylate1reservoir
350-100 mMzinc acetate1reservoir
47.5 mMNAD+1reservoir
518 %(w/v)PEG60001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 34754 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.12
Reflection
*PLUS
Highest resolution: 3 Å / Num. measured all: 79865
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 83.5 %

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Processing

Software
NameVersionClassification
X-PLORrefinement
R-AXISIIC (HAGASHI/RIGAKU)data reduction
RefinementResolution: 3→8 Å / σ(F): 1
RfactorNum. reflection
Rfree0.305 -
Rwork0.225 -
obs0.225 32781
Displacement parametersBiso mean: 19 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11393 0 232 9 11634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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
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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