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- PDB-1teh: STRUCTURE OF HUMAN LIVER CHICHI ALCOHOL DEHYDROGENASE (A GLUTATHI... -

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Basic information

Entry
Database: PDB / ID: 1teh
TitleSTRUCTURE OF HUMAN LIVER CHICHI ALCOHOL DEHYDROGENASE (A GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE)
ComponentsHUMAN CHICHI ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD+ DEPENDENT ALCOHOL DEHYDROGENASE GLUTATHIONE DEPENDENT FORMALDEHYDE DEHYDROGENASE
Function / homology
Function and homology information


formaldehyde dehydrogenase (NAD+) activity / S-nitrosoglutathione reductase (NADH) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / response to nitrosative stress / formaldehyde catabolic process / Ethanol oxidation ...formaldehyde dehydrogenase (NAD+) activity / S-nitrosoglutathione reductase (NADH) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / response to nitrosative stress / formaldehyde catabolic process / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / positive regulation of blood pressure / alcohol dehydrogenase / respiratory system process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to redox state / retinoid metabolic process / fatty acid binding / response to lipopolysaccharide / electron transfer activity / mitochondrion / extracellular exosome / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Alcohol dehydrogenase class III / 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 ...Alcohol dehydrogenase class III / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYang, Z.-N. / Hurley, T.D.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Structure of human chi chi alcohol dehydrogenase: a glutathione-dependent formaldehyde dehydrogenase.
Authors: Yang, Z.N. / Bosron, W.F. / Hurley, T.D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Structures of Three Human Beta Alcohol Dehydrogenase Variants. Correlations with Their Functional Differences
Authors: Hurley, T.D. / Bosron, W.F. / Stone, C.L. / Amzel, L.M.
History
DepositionFeb 5, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 CHICHI ALCOHOL DEHYDROGENASE
B: HUMAN CHICHI ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9369
Polymers79,2822
Non-polymers1,6547
Water63135
1
A: HUMAN CHICHI ALCOHOL DEHYDROGENASE
hetero molecules

A: HUMAN CHICHI ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8708
Polymers79,2822
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5650 Å2
ΔGint-34 kcal/mol
Surface area28100 Å2
MethodPISA, PQS
2
B: HUMAN CHICHI ALCOHOL DEHYDROGENASE
hetero molecules

B: HUMAN CHICHI ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,00110
Polymers79,2822
Non-polymers1,7198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5370 Å2
ΔGint-36 kcal/mol
Surface area28320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)141.250, 201.550, 69.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-378-

ZN

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6038, 0.0032, -0.7971), (0.0121, 0.9998, 0.0131), (0.797, -0.0176, 0.6037)
Vector: 13.701, -38.44, 7.914)

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Components

#1: Protein HUMAN CHICHI ALCOHOL DEHYDROGENASE / GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE / CLASS III ADH


Mass: 39641.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE STRUCTURE FOR HOMODIMERIC CHI ALCOHOL DEHYDROGENASE WAS SOLVED WITH ONE NAD+ PER SUBUNIT
Source: (natural) Homo sapiens (human) / Organ: LIVER
References: UniProt: P11766, alcohol dehydrogenase, EC: 1.2.1.1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / 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


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60 %
Crystal growpH: 8
Details: 15 MG/ML ENZYME IN 280 MM MES, PH 6.7, 2 MM NAD+, 8.0 % PEG8000 AT 295 K, SITTING-DROP METHOD.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5-11 mg/mlenzyme1drop
2240 mMMES1reservoir
32.0 mMNAD+1reservoir
40.01 M1reservoirZnSO4
58.0 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 22, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→60.7 Å / Num. obs: 24896 / % possible obs: 89.5 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.2 / % possible all: 67
Reflection
*PLUS
Num. measured all: 97001
Reflection shell
*PLUS
% possible obs: 67 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata reduction
SCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.283 -7 %
Rwork0.206 --
obs0.206 23718 89.2 %
Displacement parametersBiso mean: 30.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 93 35 5672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.67
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.347
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.67
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.347

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