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- PDB-7ehm: Human MTHFD2 in complex with compound 21 and 15 -

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Basic information

Entry
Database: PDB / ID: 7ehm
TitleHuman MTHFD2 in complex with compound 21 and 15
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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-J49 / Chem-J4C / Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 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)70,4116
Polymers68,3672
Non-polymers2,0444
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-20 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.232, 114.232, 114.164
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 (E. coli)
References: UniProt: P13995, methylenetetrahydrofolate dehydrogenase (NAD+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-J4C / (2S)-2-[[4-[[1-[(3,4-dichlorophenyl)methyl]-3,7-dimethyl-2,6-bis(oxidanylidene)purin-8-yl]amino]phenyl]carbonylamino]pentanedioic acid / (4-((1-(3,4-dichlorobenzyl)-3,7-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)amino)benzoyl)-L-glutamic acid


Mass: 603.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24Cl2N6O7 / 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.: 197 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
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: 2.13→30 Å / Num. obs: 47198 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Χ2: 1.059 / Net I/σ(I): 9.9 / Num. measured all: 209917
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.13-2.214.40.55547070.750.2970.6341.016100
2.21-2.294.50.39947010.8420.2120.4551.055100
2.29-2.44.50.31646940.90.1670.361.04100
2.4-2.534.50.22247340.9440.1160.2521.088100
2.53-2.684.50.16546950.970.0860.1871.094100
2.68-2.894.50.11547050.9860.0590.131.094100
2.89-3.184.50.07447300.9940.0370.0841.018100
3.18-3.644.50.05247240.9970.0260.0591.072100
3.64-4.584.40.03847330.9980.0190.0421.03699.9
4.58-304.30.03247750.9990.0160.0371.07899.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.403
Highest resolutionLowest resolution
Rotation28.56 Å2.42 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EHJ

7ehj


Resolution: 2.13→24.92 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 2281 4.84 %
Rwork0.1954 44857 -
obs0.1968 47138 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.62 Å2 / Biso mean: 45.1056 Å2 / Biso min: 23.92 Å2
Refinement stepCycle: final / Resolution: 2.13→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 142 197 4572
Biso mean--41.65 47.11 -
Num. residues----567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.180.29991480.25542777292599
2.18-2.230.27141430.244427832926100
2.23-2.280.33291300.241928262956100
2.28-2.340.25221430.241427762919100
2.34-2.410.27371390.231528212960100
2.41-2.490.29031660.226427642930100
2.49-2.580.27761630.2327732936100
2.58-2.680.28941500.226127892939100
2.68-2.810.24331520.217728122964100
2.81-2.950.25731590.216427492908100
2.95-3.140.21491410.201228332974100
3.14-3.380.22641260.206628152941100
3.38-3.720.2221060.181428442950100
3.72-4.250.19021390.174528532992100
4.26-5.340.18661210.164328192940100
5.36-24.920.20181550.17762823297899

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