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- PDB-7f3y: Wild-type Plasmodium falciparum dihydrofolate reductase-thymidyla... -

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Basic information

Entry
Database: PDB / ID: 7f3y
TitleWild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with methotrexate (MTX), NADPH and dUMP
ComponentsBifunctional dihydrofolate reductase-thymidylate synthase
KeywordsSTRUCTURAL PROTEIN / PfDHFR / methotrexate / dihydrofolate reductase / Plasmodium falciparum
Function / homology
Function and homology information


thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding / mitochondrion / cytosol
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
METHOTREXATE / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsVanichtanankul, J. / Tanramluk, D. / Yuvaniyama, J. / Yuthavong, Y.
CitationJournal: Structure / Year: 2022
Title: MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances.
Authors: Tanramluk, D. / Pakotiprapha, D. / Phoochaijaroen, S. / Chantravisut, P. / Thampradid, S. / Vanichtanankul, J. / Narupiyakul, L. / Akavipat, R. / Yuvaniyama, J.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional dihydrofolate reductase-thymidylate synthase
B: Bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,31111
Polymers143,6562
Non-polymers3,6559
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15480 Å2
ΔGint-58 kcal/mol
Surface area46680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.678, 154.403, 164.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional dihydrofolate reductase-thymidylate synthase


Mass: 71828.000 Da / Num. of mol.: 2 / Fragment: fragment 148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: DHFR-TS, dhfr-ts / Production host: Escherichia coli (E. coli) / References: UniProt: A7UD81

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Non-polymers , 5 types, 555 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#4: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 297 K / Method: microbatch / Details: PEG3350, litium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 66860 / % possible obs: 96.9 % / Redundancy: 6.6 % / CC1/2: 0.994 / Net I/σ(I): 12.5
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 6268 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QGT

3qgt


Resolution: 2.252→27.577 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.895 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.284 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2329 3247 4.999 %
Rwork0.1822 61703 -
all0.185 --
obs-64950 93.932 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.432 Å20 Å2-0 Å2
2--0.085 Å20 Å2
3---0.347 Å2
Refinement stepCycle: LAST / Resolution: 2.252→27.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 247 546 9868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178921
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.64612912
X-RAY DIFFRACTIONr_angle_other_deg1.2671.58520543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75551087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63323.786515
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.489102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.411151706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4341536
X-RAY DIFFRACTIONr_chiral_restr0.0770.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022293
X-RAY DIFFRACTIONr_nbd_refined0.2080.21828
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.28691
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24506
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2518
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.228
X-RAY DIFFRACTIONr_nbd_other0.2420.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.217
X-RAY DIFFRACTIONr_mcbond_it4.1034.2644375
X-RAY DIFFRACTIONr_mcbond_other4.1034.2654376
X-RAY DIFFRACTIONr_mcangle_it6.4766.365453
X-RAY DIFFRACTIONr_mcangle_other6.4756.3615454
X-RAY DIFFRACTIONr_scbond_it4.0934.6075171
X-RAY DIFFRACTIONr_scbond_other4.0924.6075172
X-RAY DIFFRACTIONr_scangle_it6.456.7157459
X-RAY DIFFRACTIONr_scangle_other6.4496.7157460
X-RAY DIFFRACTIONr_lrange_it9.38747.02610766
X-RAY DIFFRACTIONr_lrange_other9.39246.93510662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.252-2.3110.2721980.2273694X-RAY DIFFRACTION77.8867
2.311-2.3740.2842360.2334006X-RAY DIFFRACTION85.6624
2.374-2.4430.2922020.2124000X-RAY DIFFRACTION88.2588
2.443-2.5180.2771770.2154062X-RAY DIFFRACTION91.0634
2.518-2.6010.3382270.2213835X-RAY DIFFRACTION90.1665
2.601-2.6920.2812080.2173918X-RAY DIFFRACTION93.6876
2.692-2.7930.2621970.2073836X-RAY DIFFRACTION96.276
2.793-2.9070.2721960.1913749X-RAY DIFFRACTION97.048
2.907-3.0370.2781980.1923665X-RAY DIFFRACTION98.4957
3.037-3.1850.2461770.1843494X-RAY DIFFRACTION98.2339
3.185-3.3570.2221750.183362X-RAY DIFFRACTION98.6611
3.357-3.560.231510.183195X-RAY DIFFRACTION98.9648
3.56-3.8060.1961740.1642984X-RAY DIFFRACTION99.2458
3.806-4.110.2071380.1612800X-RAY DIFFRACTION98.69
4.11-4.5020.1821460.1462570X-RAY DIFFRACTION99.0879
4.502-5.0330.1751250.1462384X-RAY DIFFRACTION99.6426
5.033-5.8090.211080.1732102X-RAY DIFFRACTION98.9257
5.809-7.110.2321010.1861816X-RAY DIFFRACTION100
7.11-10.0360.2750.1611424X-RAY DIFFRACTION99.8668
10.036-27.5770.27380.214808X-RAY DIFFRACTION93.3775

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