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- PDB-1cwn: CRYSTAL STRUCTURE OF PORCINE ALDEHYDE REDUCTASE HOLOENZYME -

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Basic information

Entry
Database: PDB / ID: 1cwn
TitleCRYSTAL STRUCTURE OF PORCINE ALDEHYDE REDUCTASE HOLOENZYME
ComponentsALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / TIM-BARREL / NADP
Function / homology
Function and homology information


glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / Oxidoreductases; Acting on NADH or NADPH / S-nitrosoglutathione reductase (NADPH) activity / alcohol dehydrogenase (NADP+) / D-glucuronate catabolic process / L-ascorbic acid biosynthetic process / aldehyde catabolic process / methylglyoxal reductase (NADPH) (acetol producing) activity ...glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / Oxidoreductases; Acting on NADH or NADPH / S-nitrosoglutathione reductase (NADPH) activity / alcohol dehydrogenase (NADP+) / D-glucuronate catabolic process / L-ascorbic acid biosynthetic process / aldehyde catabolic process / methylglyoxal reductase (NADPH) (acetol producing) activity / cellular detoxification of aldehyde / L-glucuronate reductase activity / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / aldose reductase (NADPH) activity / lipid metabolic process / apical plasma membrane / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member A1 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member A1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsEl-Kabbani, O.
Citation
Journal: Protein Pept.Lett. / Year: 1996
Title: Crystal structure of porcine aldehyde reductase at 2.0 angstrom resolution: Modeling an inhibitor in the active site of the enzyme.
Authors: ElKabbani, O. / Carper, D.A. / McGowan, M.H. / Ginell, S.L.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of Porcine Aldehyde Reductase Holoenzyme
Authors: El-Kabbani, O. / Judge, K. / Ginell, S.L. / Myles, D.A. / Delucas, L.J. / Flynn, T.G.
History
DepositionJul 30, 1996Processing site: BNL
Revision 1.0Feb 4, 1998Provider: 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 / 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 / _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: ALDEHYDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1962
Polymers36,4531
Non-polymers7431
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.200, 67.200, 243.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ALDEHYDE REDUCTASE / ALR1 / Coordinate model: Cα atoms only


Mass: 36452.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / Tissue: MEDULLA, CORTEX / References: UniProt: P50578, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 45 %

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.00615
DetectorDetector: CCD / Date: Jun 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00615 Å / Relative weight: 1
ReflectionNum. obs: 21648 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
X-PLORrefinement
MADNESdata reduction
RefinementResolution: 2→6 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.2 -
obs0.2 20127
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms324 0 48 0 372
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_deg2.3
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_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5

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