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- PDB-6t7q: Human Aldose Reductase Mutant L301A in Complex with a Ligand with... -

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Basic information

Entry
Database: PDB / ID: 6t7q
TitleHuman Aldose Reductase Mutant L301A in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid)
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / L301A Mutant / SAR_061 ligand / transient binding pocket
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / daunorubicin metabolic process / doxorubicin metabolic process / epithelial cell maturation / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
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
Chem-4G7 / CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsHubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Aldose Reductase Mutant L301A in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid)
Authors: Hubert, L.-S. / Ley, M. / Scheer, F. / Diederich, W. / Heine, A. / Klebe, G.
History
DepositionOct 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1394
Polymers35,8561
Non-polymers1,2833
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.432, 67.109, 49.545
Angle α, β, γ (deg.)90.000, 92.192, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aldo-keto reductase family 1 member B1 / Aldehyde reductase / Aldose reductase / AR


Mass: 35856.262 Da / Num. of mol.: 1 / Mutation: L301A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase
#2: Chemical ChemComp-4G7 / 3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid


Mass: 347.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14FNO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 43.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM Di-Ammoniumhydrogen citrate pH 5.0: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 20% (w/v) PEG 6000 Soaking- ...Details: 50 mM Di-Ammoniumhydrogen citrate pH 5.0: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 20% (w/v) PEG 6000 Soaking-buffer: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 25% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.007→39.84 Å / Num. obs: 155904 / % possible obs: 95.3 % / Redundancy: 3.37 % / Biso Wilson estimate: 6.55 Å2 / CC1/2: 0.998 / Rsym value: 0.052 / Net I/σ(I): 13.84
Reflection shellResolution: 1.01→1.07 Å / Redundancy: 3.17 % / Mean I/σ(I) obs: 2.47 / Num. unique obs: 23595 / CC1/2: 0.876 / Rsym value: 0.481 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRR

4prr


Resolution: 1.01→39.84 Å / SU ML: 0.1092 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 12.0585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1322 7786 5 %
Rwork0.1177 147904 -
obs0.1184 155690 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.81 Å2
Refinement stepCycle: LAST / Resolution: 1.01→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 86 384 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692914
X-RAY DIFFRACTIONf_angle_d1.03524008
X-RAY DIFFRACTIONf_chiral_restr0.0807438
X-RAY DIFFRACTIONf_plane_restr0.0082567
X-RAY DIFFRACTIONf_dihedral_angle_d17.14981121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.020.47142380.49224504X-RAY DIFFRACTION87.8
1.02-1.030.37382510.38164770X-RAY DIFFRACTION91.71
1.03-1.040.26092490.28084726X-RAY DIFFRACTION92.56
1.04-1.060.26482480.23024706X-RAY DIFFRACTION91.86
1.06-1.070.21512440.20044641X-RAY DIFFRACTION90.8
1.07-1.090.20632540.18354826X-RAY DIFFRACTION93.42
1.09-1.10.18952550.17494847X-RAY DIFFRACTION93.99
1.1-1.120.19352560.16714861X-RAY DIFFRACTION94.94
1.12-1.140.12822550.10664853X-RAY DIFFRACTION94.7
1.14-1.150.12192590.09594912X-RAY DIFFRACTION94.78
1.15-1.170.11812580.08964906X-RAY DIFFRACTION95.4
1.17-1.20.11012570.08934876X-RAY DIFFRACTION95.25
1.2-1.220.10892520.08994805X-RAY DIFFRACTION93.11
1.22-1.240.11132630.08954981X-RAY DIFFRACTION96.26
1.24-1.270.11082610.08784968X-RAY DIFFRACTION96.58
1.27-1.30.10742590.08624924X-RAY DIFFRACTION96.14
1.3-1.330.10492600.09054939X-RAY DIFFRACTION96.17
1.33-1.370.09782660.09035051X-RAY DIFFRACTION97.01
1.37-1.410.11172620.09314979X-RAY DIFFRACTION97.31
1.41-1.450.10582630.09234988X-RAY DIFFRACTION96.95
1.45-1.510.10712600.09034947X-RAY DIFFRACTION95.7
1.51-1.570.10932660.08925063X-RAY DIFFRACTION98.07
1.57-1.640.10392690.09255107X-RAY DIFFRACTION98.17
1.64-1.720.1192660.09815054X-RAY DIFFRACTION98.65
1.72-1.830.12992690.10365114X-RAY DIFFRACTION98.46
1.83-1.970.12312670.10885073X-RAY DIFFRACTION98.2
1.97-2.170.11692640.10845003X-RAY DIFFRACTION96.86
2.17-2.490.12662720.1165174X-RAY DIFFRACTION99.51
2.49-3.130.12932710.12625141X-RAY DIFFRACTION99.08
3.13-39.840.14342720.13285165X-RAY DIFFRACTION97.75

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