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- PDB-1ae4: ALDEHYDE REDUCTASE COMPLEXED WITH COFACTOR AND INHIBITOR, ALPHA C... -

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Basic information

Entry
Database: PDB / ID: 1ae4
TitleALDEHYDE REDUCTASE COMPLEXED WITH COFACTOR AND INHIBITOR, ALPHA CARBON ATOMS ONLY
ComponentsALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / ALDO-KETO REDUCTASE / TIM-BARREL
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 / TOLRESTAT / Aldo-keto reductase family 1 member A1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / DIFFERENCE-FOURIER / Resolution: 2.4 Å
AuthorsEl-Kabbani, O.
Citation
Journal: Proteins / Year: 1997
Title: Studies on the inhibitor-binding site of porcine aldehyde reductase: crystal structure of the holoenzyme-inhibitor ternary complex.
Authors: el-Kabbani, O. / Carper, D.A. / McGowan, M.H. / Devedjiev, Y. / Rees-Milton, K.J. / Flynn, T.G.
#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
DepositionMar 5, 1997Processing site: BNL
Revision 1.0Mar 11, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)37,6853
Polymers36,5841
Non-polymers1,1012
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.800, 67.800, 245.280
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: 36583.883 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
#3: Chemical ChemComp-TOL / TOLRESTAT


Mass: 357.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F3NO3S

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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: 2.24 Å3/Da / Density % sol: 43 %
Description: THE POSITION OF BOUND INHIBITOR WAS DETERMINED FROM A DIFFERENCE ELECTRON DENSITY MAP.
Crystal growpH: 8.9 / Details: BUFFERED AMMONIUM SULFATE SOLUTION, PH 8.9
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlprotein1drop
25 mM2-mercaptoethanol1reservoir
35 mMTris-HCl1reservoir
449 mMNADPH1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 13319 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 21.2
Reflection
*PLUS
Num. all: 14296 / Num. measured all: 91887

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE-FOURIER
Starting model: PORCINE ALDEHYDE REDUCTASE IN COMPLEX WITH COENZYME

Resolution: 2.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.19 --
obs0.19 10907 86 %
Displacement parametersBiso mean: 20.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms324 0 72 0 396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.4
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
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.29 588 -
obs--35 %

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