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Yorodumi- PDB-7ewh: Crystal structure of human PHGDH in complex with Homoharringtonine -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ewh | |||||||||
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Title | Crystal structure of human PHGDH in complex with Homoharringtonine | |||||||||
Components | D-3-phosphoglycerate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / inhibitor | |||||||||
Function / homology | Function and homology information gamma-aminobutyric acid metabolic process / threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase ...gamma-aminobutyric acid metabolic process / threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase / L-serine biosynthetic process / L-malate dehydrogenase activity / G1 to G0 transition / neural tube development / spinal cord development / glutamine metabolic process / brain development / neuron projection development / NAD binding / regulation of gene expression / electron transfer activity / extracellular exosome / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | |||||||||
Authors | Hsieh, C.H. / Cheng, Y.S. / Lee, Y.S. / Huang, H.C. / Juan, H.F. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Biomed Pharmacother / Year: 2023 Title: Homoharringtonine as a PHGDH inhibitor: Unraveling metabolic dependencies and developing a potent therapeutic strategy for high-risk neuroblastoma. Authors: Hsieh, C.H. / Huang, C.T. / Cheng, Y.S. / Hsu, C.H. / Hsu, W.M. / Chung, Y.H. / Liu, Y.L. / Yang, T.S. / Chien, C.Y. / Lee, Y.H. / Huang, H.C. / Juan, H.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ewh.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ewh.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ewh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/7ewh ftp://data.pdbj.org/pub/pdb/validation_reports/ew/7ewh | HTTPS FTP |
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-Related structure data
Related structure data | 2g76S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 5 - 306 / Label seq-ID: 1 - 302
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-Components
#1: Protein | Mass: 32454.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHGDH, PGDH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O43175, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase, malate dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 mM MMT buffer, pH 7.0 with 30% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→27.555 Å / Num. obs: 9221 / % possible obs: 75.95 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.136 / Rsym value: 0.159 / Net I/σ(I): 9.002 |
Reflection shell | Resolution: 2.99→3.097 Å / Num. unique obs: 481 / CC1/2: 0.899 / Rpim(I) all: 0.281 / Rrim(I) all: 0.529 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G76 Resolution: 2.99→27.555 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 39.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.72 Å2 / Biso mean: 56.0406 Å2 / Biso min: 13.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.99→27.555 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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