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- PDB-7ehn: Human MTHFD2 in complex with compound 21 and 9 -

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Basic information

Entry
Database: PDB / ID: 7ehn
TitleHuman MTHFD2 in complex with compound 21 and 9
ComponentsBifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
KeywordsOXIDOREDUCTASE / MTHFD2 / methylenetetrahydrofolate dehydrogenase 2 / 1C metabolism / mitocondria
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NAD+) / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate biosynthetic process / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / phosphate ion binding ...methylenetetrahydrofolate dehydrogenase (NAD+) / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate biosynthetic process / 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 / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily ...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 / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J49 / Chem-J4F / Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLee, L.C. / Peng, Y.H. / Wu, S.Y.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Xanthine Derivatives Reveal an Allosteric Binding Site in Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2).
Authors: Lee, L.C. / Peng, Y.H. / Chang, H.H. / Hsu, T. / Lu, C.T. / Huang, C.H. / Hsueh, C.C. / Kung, F.C. / Kuo, C.C. / Jiaang, W.T. / Wu, S.Y.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)70,2506
Polymers68,3672
Non-polymers1,8834
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-20 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.169, 113.169, 113.670
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: 34183.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTHFD2, NMDMC / Plasmid: pET14b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P13995, methylenetetrahydrofolate dehydrogenase (NAD+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-J4F / 3-[4-[[1-[(4-chloranyl-1H-indol-2-yl)methyl]-3,7-dimethyl-2,6-bis(oxidanylidene)purin-8-yl]amino]-6-methyl-pyrimidin-2-yl]propanoic acid / 3-(4-((1-((4-chloro-1H-indol-2-yl)methyl)-3,7-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)amino)-6-methylpyrimidin-2-yl)propanoic acid


Mass: 522.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23ClN8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-J49 / (2S)-2-[[4-[(4-azanyl-6-oxidanyl-pyrimidin-5-yl)carbamoylamino]phenyl]carbonylamino]pentanedioic acid / (4-(3-(4-amino-6-hydroxypyrimidin-5-yl)ureido)benzoyl)-L-glutamic acid


Mass: 418.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N6O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.88 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: isopropanol, bis-Tris pH 7.1, PEG 200, PEG 3350, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 6, 2019 / Details: A Pair of K-B Focusing Mirrors
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 38105 / % possible obs: 97.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Χ2: 1.057 / Net I/σ(I): 11 / Num. measured all: 111840
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.332.90.52238290.7520.3520.6331.03298.7
2.33-2.422.90.3838400.8580.2530.4591.02698.8
2.42-2.532.90.27938480.9190.1840.3361.07299
2.53-2.672.90.20438570.9490.1340.2451.04999
2.67-2.832.90.14938350.9750.0980.181.06298.8
2.83-3.052.90.10538550.9830.0690.1271.07398.8
3.05-3.362.90.07738050.9880.0490.0921.09398.2
3.36-3.8530.06538320.990.0410.0781.04697.4
3.85-4.8430.0637500.9910.0370.0711.04296.1
4.84-3030.06136540.9910.0390.0731.07791.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.412
Highest resolutionLowest resolution
Rotation29.98 Å2.59 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-20002.3.10data reduction
SCALEPACKdata scaling
MOLREP11.7.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EHM

7ehm


Resolution: 2.25→25.39 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1987 5.22 %
Rwork0.2005 36108 -
obs0.2025 38095 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.39 Å2 / Biso mean: 51.6479 Å2 / Biso min: 29.58 Å2
Refinement stepCycle: final / Resolution: 2.25→25.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 134 122 4478
Biso mean--43.91 49.33 -
Num. residues----566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.310.35261280.2752537266595
2.31-2.370.31111390.2552591273099
2.37-2.440.31251580.24932586274499
2.44-2.520.29691280.24792649277799
2.52-2.610.26221510.24472582273399
2.61-2.710.32741260.23972615274199
2.71-2.840.29661710.23222600277199
2.84-2.990.30921510.23392607275899
2.99-3.170.27421500.21452577272799
3.17-3.420.26351560.21232604276098
3.42-3.760.23931240.19562578270297
3.76-4.30.20691140.17752587270197
4.3-5.410.20371360.1722551268795
5.41-25.390.18181550.17432444259991

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