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- PDB-8t4p: Human mitochondrial serine hydroxymethyltransferase (SHMT2) in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t4p | ||||||
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Title | Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and di-glutamate AGF347 inhibitor | ||||||
![]() | Serine hydroxymethyltransferase, mitochondrial | ||||||
![]() | TRANSFERASE / Mitochondrial / one-carbon metabolism / polyglutamate / inhibitor / complex / serine and glycine metabolism | ||||||
Function / homology | ![]() BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines ...BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / regulation of oxidative phosphorylation / 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 / protein tetramerization / microtubule cytoskeleton / pyridoxal phosphate binding / one-carbon metabolic process / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / chromatin binding / positive regulation of cell population proliferation / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Katinas, J.M. / Dann III, C.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2. Authors: Katinas, J.M. / Nayeen, M.J. / Schneider, M. / Shah, K. / Fifer, A.N. / Klapper, L.M. / Sharma, A. / Thalluri, K. / Van Nieuwenhze, M.S. / Hou, Z. / Gangjee, A. / Matherly, L.H. / Dann 3rd, C.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365.3 KB | Display | ![]() |
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PDB format | ![]() | 297.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gksC ![]() 8gktC ![]() 8gkuC ![]() 8gkwC ![]() 8gkyC ![]() 8gkzC ![]() 8t4oC ![]() 8tlcC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54635.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: First 31 residues are part of the hexa-His tag and TEV protease site. Any additional residue to A mutations are due to lack of density in the side chain. Any missing residues are due to lack ...Details: First 31 residues are part of the hexa-His tag and TEV protease site. Any additional residue to A mutations are due to lack of density in the side chain. Any missing residues are due to lack of density in the backbone or side chain and inability to model a specific conformation. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P34897, glycine hydroxymethyltransferase #2: Chemical | #3: Chemical | ChemComp-Y5Z / | Mass: 602.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H31FN6O9 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.84 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 7.5 Details: 20 mM sodium phosphate pH 7.5, 100 mM NaCl, 0.2 mM EDTA, and 0.5 mM TCEP and PLP loaded His-SHMT2 concentrated to 0.01 to 0.02 mM |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Nov 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.791 Å / Num. obs: 203843 / % possible obs: 92 % / Redundancy: 5.7 % / CC1/2: 0.98 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.8→2.93 Å / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 26923 / CC1/2: 0.755 / Rpim(I) all: 0.318 / Rrim(I) all: 0.772 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→48.791 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -19.9072 Å / Origin y: 65.6476 Å / Origin z: 6.8826 Å
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Refinement TLS group | Selection details: all |