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- PDB-5l4n: Leishmania major Pteridine reductase 1 (PTR1) in complex with com... -

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Basic information

Entry
Database: PDB / ID: 5l4n
TitleLeishmania major Pteridine reductase 1 (PTR1) in complex with compound 1
ComponentsPteridine reductase 1
KeywordsOXIDOREDUCTASE / Leishmania major / Pteridine reductase 1 / PTR1
Function / homology
Function and homology information


pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
Chem-6QT / ACETATE ION / Chem-NDP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Pteridine reductase 1
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDello Iacono, L. / Di Pisa, F. / Pozzi, C. / Landi, G. / Mangani, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Union603240 Italy
CitationJournal: Molecules / Year: 2017
Title: Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.
Authors: Di Pisa, F. / Landi, G. / Dello Iacono, L. / Pozzi, C. / Borsari, C. / Ferrari, S. / Santucci, M. / Santarem, N. / Cordeiro-da-Silva, A. / Moraes, C.B. / Alcantara, L.M. / Fontana, V. / ...Authors: Di Pisa, F. / Landi, G. / Dello Iacono, L. / Pozzi, C. / Borsari, C. / Ferrari, S. / Santucci, M. / Santarem, N. / Cordeiro-da-Silva, A. / Moraes, C.B. / Alcantara, L.M. / Fontana, V. / Freitas-Junior, L.H. / Gul, S. / Kuzikov, M. / Behrens, B. / Pohner, I. / Wade, R.C. / Costi, M.P. / Mangani, S.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Pteridine reductase 1
B: Pteridine reductase 1
C: Pteridine reductase 1
D: Pteridine reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,91417
Polymers121,8264
Non-polymers4,08813
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21620 Å2
ΔGint-110 kcal/mol
Surface area34850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.699, 104.250, 137.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pteridine reductase 1 / / H region methotrexate resistance protein


Mass: 30456.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: PTR1, HMTXR, L1063.01, LmjF23.0270, LmjF_23_0270 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01782, pteridine reductase

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Non-polymers , 8 types, 576 molecules

#2: Chemical ChemComp-6QT / (2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one


Mass: 256.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: Orthorhombic crystals (clusters)
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 12.5 mg/mL in 20 mM Sodium Acetate pH5.3 and 10 mM DTT. Crystallisation buffer: 12% PEG 4600, 100 mM Sodium Acetate buffer pH 5.5 and 120-160 mM Calcium Acetate
PH range: 5.3-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2014
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→94.7 Å / Num. obs: 54151 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BFA

2bfa


Resolution: 2.35→82.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.834 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 2714 5 %RANDOM
Rwork0.16303 ---
obs0.16574 51393 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.154 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→82.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 266 563 8417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.878211275
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76551087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97922.347277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.085151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1591554
X-RAY DIFFRACTIONr_chiral_restr0.1120.21351
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216096
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.1622.344207
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4813.4785252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4922.4964002
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.1819.80513281
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 168 -
Rwork0.224 3869 -
obs--96.86 %

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