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- PDB-1d1s: WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1d1s
TitleWILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE
ComponentsALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
KeywordsOXIDOREDUCTASE / ROSSMAN OR DINUCLEOTIDE FOLD
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 / CACODYLATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / All-trans-retinol dehydrogenase [NAD(+)] ADH7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsXie, P.T. / Hurley, T.D.
Citation
Journal: Protein Sci. / Year: 1999
Title: Methionine-141 directly influences the binding of 4-methylpyrazole in human sigma sigma alcohol dehydrogenase.
Authors: Xie, P.T. / Hurley, T.D.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: X-ray structure of human class IV sigma-sigma alcohol dehydrogenase
Authors: Xie, P.T. / Parsons, S.H. / Speckhard, D.C. / Bosron, W.F. / Hurley, T.D.
History
DepositionSep 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 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_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_asym_id / _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.ptnr1_symmetry / _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: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
B: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
C: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
D: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,04645
Polymers159,6974
Non-polymers5,34941
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
hetero molecules

D: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,79125
Polymers79,8492
Non-polymers2,94223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6410 Å2
ΔGint-342 kcal/mol
Surface area29830 Å2
MethodPISA
3
A: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
B: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,93426
Polymers79,8492
Non-polymers3,08624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-314 kcal/mol
Surface area27010 Å2
MethodPISA, PQS
4
C: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
D: ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN
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 area7480 Å2
ΔGint-218 kcal/mol
Surface area27370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.4, 90.9, 121.1
Angle α, β, γ (deg.)90, 99.6, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN / RETINOL DEHYDROGENASE / GASTRIC ALCOHOL DEHYDROGENASE


Mass: 39924.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P40394, alcohol dehydrogenase

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Non-polymers , 5 types, 449 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 MM CACODYLATE, 100 MM ZINC ACETATE, 7.5 MM NAD+, 18% POLYETHYLENE GLYCOL 6000, 8 MG/ML ENZYME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMcacodylate11
2100 mMzinc acetate11
37.5 mMNAD+11
418 %(w/v)PEG600011
58 mg/mlprotein11

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 64199 / Num. obs: 58678 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.33 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.368 / % possible all: 76
Reflection
*PLUS
Num. measured all: 254379
Reflection shell
*PLUS
% possible obs: 76 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→50 Å / σ(F): 0.5 / σ(I): 0.5 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4166 -RANDOM
Rwork0.217 ---
obs0.22 58662 91.4 %-
all-64199 --
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11156 0 272 408 11836
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_deg1.51
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 / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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