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- PDB-6t3p: Human Aldose Reductase Mutant L300A in Complex with a Ligand with... -

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Basic information

Entry
Database: PDB / ID: 6t3p
TitleHuman Aldose Reductase Mutant L300A in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid)
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / L300A Mutant / Complex with IDD / Opened Transient Binding Pocket
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / 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 / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / epithelial cell maturation / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / renal water homeostasis / 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-30L / 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: 0.97 Å
AuthorsHubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Aldose Reductase Mutant L300A in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid)
Authors: Hubert, L.-S. / Ley, M. / Scheer, F. / Diederich, W. / Heine, A. / Klebe, G.
History
DepositionOct 11, 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)37,4885
Polymers35,8561
Non-polymers1,6324
Water9,098505
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-5 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.531, 67.111, 49.402
Angle α, β, γ (deg.)90.000, 92.462, 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: L300A
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-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-30L / {5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid


Mass: 348.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13FN2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 505 / 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: 43.61 %
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% 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: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.946→49.36 Å / Num. obs: 191423 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 4.85 Å2 / CC1/2: 0.999 / Rsym value: 0.042 / Net I/σ(I): 17.33
Reflection shellResolution: 0.95→1 Å / Redundancy: 3.1 % / Num. unique obs: 29134 / CC1/2: 0.835 / Rsym value: 0.567 / % possible all: 91.9

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Processing

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

4prr


Resolution: 0.97→49.36 Å / SU ML: 0.1109 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 9.6195
RfactorNum. reflection% reflection
Rfree0.1151 8981 5 %
Rwork0.105 --
obs0.1055 179575 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 9.7 Å2
Refinement stepCycle: LAST / Resolution: 0.97→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 111 505 3113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712970
X-RAY DIFFRACTIONf_angle_d1.05094087
X-RAY DIFFRACTIONf_chiral_restr0.2447439
X-RAY DIFFRACTIONf_plane_restr0.0086591
X-RAY DIFFRACTIONf_dihedral_angle_d18.88271172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.54592900.51525513X-RAY DIFFRACTION96.8
0.98-0.990.40732940.3885580X-RAY DIFFRACTION96.23
0.99-10.26592920.27875542X-RAY DIFFRACTION96.13
1-1.020.18522930.20635565X-RAY DIFFRACTION96.1
1.02-1.030.16972950.15575601X-RAY DIFFRACTION96.43
1.03-1.040.14382870.13675448X-RAY DIFFRACTION95.71
1.04-1.060.14182970.13465637X-RAY DIFFRACTION97.84
1.06-1.080.14352990.1385677X-RAY DIFFRACTION97.68
1.08-1.090.15972960.14875625X-RAY DIFFRACTION98.16
1.09-1.110.092980.08185661X-RAY DIFFRACTION97.9
1.11-1.130.09453020.07715733X-RAY DIFFRACTION98.39
1.13-1.150.09012970.07435637X-RAY DIFFRACTION98.13
1.15-1.170.08792980.07385659X-RAY DIFFRACTION97.38
1.17-1.20.09263000.07295708X-RAY DIFFRACTION99.06
1.2-1.220.09073030.0725761X-RAY DIFFRACTION99.62
1.22-1.250.08093040.07125774X-RAY DIFFRACTION99.53
1.25-1.280.07853010.07445713X-RAY DIFFRACTION99.08
1.28-1.320.08533020.07975741X-RAY DIFFRACTION99.16
1.32-1.350.09992990.08415679X-RAY DIFFRACTION98.81
1.35-1.40.09933010.08765731X-RAY DIFFRACTION98.21
1.4-1.450.08863000.08535691X-RAY DIFFRACTION98.63
1.45-1.510.08953030.07845762X-RAY DIFFRACTION99.7
1.51-1.570.08843040.07975775X-RAY DIFFRACTION99.66
1.57-1.660.09993040.08595777X-RAY DIFFRACTION99.41
1.66-1.760.1063030.09385746X-RAY DIFFRACTION98.58
1.76-1.90.11383000.09725700X-RAY DIFFRACTION98.14
1.9-2.090.10792990.10265680X-RAY DIFFRACTION98.5
2.09-2.390.10463070.10095839X-RAY DIFFRACTION99.84
2.39-3.010.11733060.11155807X-RAY DIFFRACTION99.69
3.01-49.360.12893070.11735832X-RAY DIFFRACTION98.18

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