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- PDB-3h4g: Structure of aldehyde reductase holoenzyme in complex with potent... -

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Basic information

Entry
Database: PDB / ID: 3h4g
TitleStructure of aldehyde reductase holoenzyme in complex with potent aldose reductase inhibitor Fidarestat: Implications for inhibitor binding and selectivity
ComponentsAlcohol dehydrogenase [NADP+]
KeywordsOXIDOREDUCTASE / TIM BARREL / ALDO-KETO REDUCTASE / TERNARY COMPLEX / NADP
Function / homology
Function and homology information


glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / methylglyoxal reductase (NADPH) (acetol producing) activity / D-glucuronate catabolic process / alcohol dehydrogenase (NADP+) / aldehyde catabolic process / cellular detoxification of aldehyde / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity ...glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / methylglyoxal reductase (NADPH) (acetol producing) activity / D-glucuronate catabolic process / alcohol dehydrogenase (NADP+) / aldehyde catabolic process / cellular detoxification of aldehyde / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / L-ascorbic acid biosynthetic process / 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. / NADP-dependent oxidoreductase domain / 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 ...Aldo-keto reductase family 1 member A1 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-FID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member A1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCarbone, V. / El-Kabbani, O.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Structure of aldehyde reductase holoenzyme in complex with the potent aldose reductase inhibitor fidarestat: implications for inhibitor binding and selectivity
Authors: El-Kabbani, O. / Carbone, V. / Darmanin, C. / Oka, M. / Mitschler, A. / Podjarny, A. / Schulze-Briese, C. / Chung, R.P.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 5, 2009ID: 2AO0
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 [NADP+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7464
Polymers36,6271
Non-polymers1,1193
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.301, 67.301, 244.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

21A-2201-

HOH

31A-2264-

HOH

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Components

#1: Protein Alcohol dehydrogenase [NADP+] / Aldehyde reductase / Aldo-keto reductase family 1 member A1


Mass: 36626.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: kidney / References: UniProt: P50578, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-FID / (2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE / FIDARESTAT / Fidarestat


Mass: 279.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10FN3O4 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PUBLISHED SEQUENCE IS FROM EXPRESSED MATERIAL WHILE THE SEQUENCE FOR THIS ENTRY IS FROM ...THE PUBLISHED SEQUENCE IS FROM EXPRESSED MATERIAL WHILE THE SEQUENCE FOR THIS ENTRY IS FROM PURIFIED MATERIAL. O.EL-KABBANI,N.C.GREEN,G.LIN,M.CARSON,S.V.L.NARAYANA, K.M.MOORE,T.G.FLYNN,L.J.DELUCAS. STRUCTURES OF HUMAN AND PORCINE ALDEHYDE REDUCTASE: AN ENZYME IMPLICATED IN DIABETIC COMPLICATIONS. ACTA CRYSTALLOGRAPHICA D50, 859-868, 1994.

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 2M ammonium sulphate, 0.1M tris, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 29272 / Num. obs: 26755 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A0O

2a0o
PDB Unreleased entry


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.781 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / ESU R: 0.165 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1365 5.1 %RANDOM
Rwork0.18296 ---
obs0.18469 25362 91.67 %-
all-26727 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20.64 Å20 Å2
2--1.28 Å20 Å2
3----1.92 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 73 255 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222762
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9983779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91823.659123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9861520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022085
X-RAY DIFFRACTIONr_nbd_refined0.2020.21397
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21892
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.227
X-RAY DIFFRACTIONr_mcbond_it0.5111.51671
X-RAY DIFFRACTIONr_mcangle_it0.89122656
X-RAY DIFFRACTIONr_scbond_it1.17831252
X-RAY DIFFRACTIONr_scangle_it1.7974.51119
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 102 -
Rwork0.213 1777 -
obs--89.86 %

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