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- PDB-6qvg: Human SHMT2 in complex with lometrexol -

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Basic information

Entry
Database: PDB / ID: 6qvg
TitleHuman SHMT2 in complex with lometrexol
ComponentsSerine hydroxymethyltransferase, mitochondrial
KeywordsTRANSFERASE
Function / homology
Function and homology information


BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / glycine metabolic process / L-serine metabolic process / regulation of oxidative phosphorylation / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine ...BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / glycine metabolic process / L-serine metabolic process / regulation of oxidative phosphorylation / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / amino acid binding / mitochondrial nucleoid / RHOG GTPase cycle / Mitochondrial protein degradation / one-carbon metabolic process / protein tetramerization / pyridoxal phosphate binding / microtubule cytoskeleton / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / positive regulation of cell population proliferation / chromatin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ACETATE ION / 5,10-DIDEAZATETRAHYDROFOLIC ACID / GLYCINE / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsScaletti, E. / Jemth, A.S. / Helleday, T. / Stenmark, P.
CitationJournal: Febs Lett. / Year: 2019
Title: Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.
Authors: Scaletti, E. / Jemth, A.S. / Helleday, T. / Stenmark, P.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,07013
Polymers112,1362
Non-polymers1,93511
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-54 kcal/mol
Surface area30710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.807, 158.807, 208.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 56067.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli (E. coli)
References: UniProt: P34897, glycine hydroxymethyltransferase

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Non-polymers , 8 types, 379 molecules

#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DDF / 5,10-DIDEAZATETRAHYDROFOLIC ACID


Mass: 443.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M Bis-tris pH 6.5, 28 % PEGMME2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.32→208.3 Å / Num. obs: 2640873 / % possible obs: 99.8 % / Redundancy: 39.3 % / Net I/σ(I): 14.7
Reflection shellResolution: 2.32→208.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→208.26 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.081 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 3369 5 %RANDOM
Rwork0.1993 ---
obs0.20112 63841 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.101 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 2.32→208.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7087 0 130 368 7585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197382
X-RAY DIFFRACTIONr_bond_other_d0.0020.026919
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9839978
X-RAY DIFFRACTIONr_angle_other_deg0.9652.99715986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16622.899338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.646151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1661572
X-RAY DIFFRACTIONr_chiral_restr0.080.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021561
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_it1.6763.6063638
X-RAY DIFFRACTIONr_mcbond_other1.6753.6053636
X-RAY DIFFRACTIONr_mcangle_it2.8175.3994541
X-RAY DIFFRACTIONr_mcangle_other2.8175.44542
X-RAY DIFFRACTIONr_scbond_it1.7813.8933742
X-RAY DIFFRACTIONr_scbond_other1.783.8913741
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0795.7255438
X-RAY DIFFRACTIONr_long_range_B_refined5.30342.2988259
X-RAY DIFFRACTIONr_long_range_B_other5.30342.2998260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 230 -
Rwork0.339 4648 -
obs--99.41 %

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