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- PDB-1ht0: HUMAN GAMMA-2 ALCOHOL DEHYDROGENSE -

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Basic information

Entry
Database: PDB / ID: 1ht0
TitleHUMAN GAMMA-2 ALCOHOL DEHYDROGENSE
ComponentsCLASS I ALCOHOL DEHYDROGENASE 3, GAMMA SUBUNIT
KeywordsOXIDOREDUCTASE / rossmann fold / alcohol dehydrogenase / zinc
Function / homology
Function and homology information


Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / RA biosynthesis pathway / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding ...Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / RA biosynthesis pathway / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol 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 / Alcohol dehydrogenase 1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNiederhut, M.S. / Gibbons, B.J. / Perez-Miller, S. / Hurley, T.D.
CitationJournal: Protein Sci. / Year: 2001
Title: Three-dimensional structures of the three human class I alcohol dehydrogenases.
Authors: Niederhut, M.S. / Gibbons, B.J. / Perez-Miller, S. / Hurley, T.D.
History
DepositionDec 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLASS I ALCOHOL DEHYDROGENASE 3, GAMMA SUBUNIT
B: CLASS I ALCOHOL DEHYDROGENASE 3, GAMMA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0758
Polymers79,4872
Non-polymers1,5886
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-115 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.4, 71.5, 92.1
Angle α, β, γ (deg.)90, 102.9, 90
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Detailsbiological dimer is within the asymmetric unit

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Components

#1: Protein CLASS I ALCOHOL DEHYDROGENASE 3, GAMMA SUBUNIT / E.C.1.1.1.1 / ALCOHOL DEHYDROGENASE (CLASS I) / GAMMA POLYPEPTIDE / ALDEHYDE REDUCTASE / ALCOHOL DEHYDROGENASE 3 ...ALCOHOL DEHYDROGENASE (CLASS I) / GAMMA POLYPEPTIDE / ALDEHYDE REDUCTASE / ALCOHOL DEHYDROGENASE 3 (CLASS I) / GAMMA POLYPEPTIDE / ALCOHOL DEHYDROGENASE GAMMA CHAIN


Mass: 39743.266 Da / Num. of mol.: 2 / Fragment: GAMMA SUBUNIT / Mutation: POLYMORPHIC VARIANT WITH Q271 AND V349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADH3 OR ADH1C*2 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P00326, 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100 mM Tris, 4 mM NAD+, 18% PEG 6000, 10 mg/ml protein, pH 9.0, VAPOR DIFFUSION, SITTING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG600011
250 mMTris-HCl11
34 mMNAD+11
410 mg/mlprotein11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 31, 1998 / Details: yale focusing mirrors
RadiationMonochromator: yale focusing mirrors with nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. all: 48663 / Num. obs: 47641 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.7 / % possible all: 86.8
Reflection
*PLUS
Num. measured all: 188548
Reflection shell
*PLUS
% possible obs: 86.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DEH

1deh


Resolution: 2→44 Å / Isotropic thermal model: isotropic individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3376 7.1 %random
Rwork0.193 ---
all0.196 48663 --
obs0.196 47641 --
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 92 650 6298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_improper_angle_d1.4
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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