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- PDB-6i6f: SEPIAPTERIN REDUCTASE IN COMPLEX WITH COMPOUND 1 -

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Basic information

Entry
Database: PDB / ID: 6i6f
TitleSEPIAPTERIN REDUCTASE IN COMPLEX WITH COMPOUND 1
ComponentsSepiapterin reductase
KeywordsOXIDOREDUCTASE / SEPIAPTERIN-REDUCTASE / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) / sepiapterin reductase (NADP+) activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Sepiapterin reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ethyl 4-azanyl-3-bromanyl-benzoate / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Sepiapterin reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsAlen, J. / Schade, M. / Wagener, M. / Blaesse, M.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Fragment-Based Discovery of Novel Potent Sepiapterin Reductase Inhibitors.
Authors: Alen, J. / Schade, M. / Wagener, M. / Christian, F. / Nordhoff, S. / Merla, B. / Dunkern, T.R. / Bahrenberg, G. / Ratcliffe, P.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sepiapterin reductase
B: Sepiapterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,43518
Polymers59,8972
Non-polymers2,53816
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-11 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.154, 77.194, 114.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sepiapterin reductase / SPR


Mass: 29948.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-H4E / ethyl 4-azanyl-3-bromanyl-benzoate


Mass: 244.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10BrNO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 20.00 %w/v PEG 3350, 0.10 M BIS-TRIS PROP PH 6.50, 0.10 M NABR

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→64.07 Å / Num. obs: 37878 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 16.73
Reflection shellResolution: 1.94→2.19 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.113 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→64.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.708 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 2044 5.4 %RANDOM
Rwork0.19082 ---
obs0.19298 35807 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---0.72 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.94→64.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 161 206 4294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194169
X-RAY DIFFRACTIONr_bond_other_d0.0040.024118
X-RAY DIFFRACTIONr_angle_refined_deg1.5522.0395655
X-RAY DIFFRACTIONr_angle_other_deg1.17839446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53624.214159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.81615700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1371531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214667
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6183.3432106
X-RAY DIFFRACTIONr_mcbond_other2.6183.3432105
X-RAY DIFFRACTIONr_mcangle_it3.5075.6172631
X-RAY DIFFRACTIONr_mcangle_other3.5065.6172632
X-RAY DIFFRACTIONr_scbond_it3.4043.7612063
X-RAY DIFFRACTIONr_scbond_other3.3993.7612063
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8866.1233012
X-RAY DIFFRACTIONr_long_range_B_refined6.3130.844435
X-RAY DIFFRACTIONr_long_range_B_other6.27630.774414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.941→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 137 -
Rwork0.24 2646 -
obs--96.13 %

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