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- PDB-6jib: Human MTHFD2 in complex with DS44960156 -

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Basic information

Entry
Database: PDB / ID: 6jib
TitleHuman MTHFD2 in complex with DS44960156
ComponentsBifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
KeywordsOXIDOREDUCTASE / INHIBITOR / FOLATE / COFACTOR / DEHYDROGENASE
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NAD+) / methylenetetrahydrofolate dehydrogenase (NAD+) activity / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / phosphate ion binding / folic acid metabolic process ...methylenetetrahydrofolate dehydrogenase (NAD+) / methylenetetrahydrofolate dehydrogenase (NAD+) activity / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / phosphate ion binding / folic acid metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / extracellular space
Similarity search - Function
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-BQF / PHOSPHATE ION / Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSuzuki, M. / Matsui, Y. / Kawai, J.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure-Based Design and Synthesis of an Isozyme-Selective MTHFD2 Inhibitor with a Tricyclic Coumarin Scaffold.
Authors: Kawai, J. / Ota, M. / Ohki, H. / Toki, T. / Suzuki, M. / Shimada, T. / Matsui, S. / Inoue, H. / Sugihara, C. / Matsuhashi, N. / Matsui, Y. / Takaishi, S. / Nakayama, K.
History
DepositionFeb 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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: Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
B: Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47913
Polymers70,4312
Non-polymers2,04811
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-33 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.424, 116.424, 113.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial


Mass: 35215.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTHFD2, NMDMC / Production host: Escherichia coli (E. coli)
References: UniProt: P13995, methylenetetrahydrofolate dehydrogenase (NAD+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical
ChemComp-BQF / 4-(5-oxo-1,5-dihydro-2H-[1]benzopyrano[3,4-c]pyridine-3(4H)-carbonyl)benzoic acid


Mass: 349.337 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H15NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28% i-PrOH, 0.1M bis-Tris, pH 6.5, 3% PEG 200, 10 mM spermidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.05 Å / Num. obs: 41331 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.032 / Rrim(I) all: 0.104 / Net I/σ(I): 13.8 / Num. measured all: 354192 / Scaling rejects: 880
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.314.20.93732070.5740.5291.0899.6
9.81-46.0510.60.0885240.9460.0290.09399

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DIA

1dia


Resolution: 2.25→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.389 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.193 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 2147 5.2 %RANDOM
Rwork0.2009 ---
obs0.2031 39113 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 152.34 Å2 / Biso mean: 50.704 Å2 / Biso min: 26.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å2-0 Å2
2--1.44 Å20 Å2
3----4.67 Å2
Refinement stepCycle: final / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 144 141 4660
Biso mean--59.05 49.21 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124615
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.6656278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28622.895190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00215775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2451525
X-RAY DIFFRACTIONr_chiral_restr0.1050.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023424
LS refinement shellResolution: 2.25→2.328 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.345 187 -
Rwork0.311 3829 -
all-4016 -
obs--99.63 %

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