+Open data
-Basic information
Entry | Database: PDB / ID: 6rj2 | ||||||
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Title | Crystal structure of PHGDH in complex with compound 40 | ||||||
Components | D-3-phosphoglycerate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Protein-Ligand complex / Dehydrogenase | ||||||
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 Å | ||||||
Authors | Bader, G. / Wolkerstorfer, B. / Zoephel, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Intracellular Trapping of the Selective Phosphoglycerate Dehydrogenase (PHGDH) InhibitorBI-4924Disrupts Serine Biosynthesis. Authors: Weinstabl, H. / Treu, M. / Rinnenthal, J. / Zahn, S.K. / Ettmayer, P. / Bader, G. / Dahmann, G. / Kessler, D. / Rumpel, K. / Mischerikow, N. / Savarese, F. / Gerstberger, T. / Mayer, M. / ...Authors: Weinstabl, H. / Treu, M. / Rinnenthal, J. / Zahn, S.K. / Ettmayer, P. / Bader, G. / Dahmann, G. / Kessler, D. / Rumpel, K. / Mischerikow, N. / Savarese, F. / Gerstberger, T. / Mayer, M. / Zoephel, A. / Schnitzer, R. / Sommergruber, W. / Martinelli, P. / Arnhof, H. / Peric-Simov, B. / Hofbauer, K.S. / Garavel, G. / Scherbantin, Y. / Mitzner, S. / Fett, T.N. / Scholz, G. / Bruchhaus, J. / Burkard, M. / Kousek, R. / Ciftci, T. / Sharps, B. / Schrenk, A. / Harrer, C. / Haering, D. / Wolkerstorfer, B. / Zhang, X. / Lv, X. / Du, A. / Li, D. / Li, Y. / Quant, J. / Pearson, M. / McConnell, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rj2.cif.gz | 245.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rj2.ent.gz | 196.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/6rj2 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/6rj2 | HTTPS FTP |
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-Related structure data
Related structure data | 6cwaC 6rihC 6rj3C 6rj5C 6rj6C 2g76S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33630.762 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 (E. coli) References: UniProt: O43175, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase, malate dehydrogenase #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 25 % PEG 8000, 0.1 M MES, 0.2 M Lithium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→65.65 Å / Num. obs: 41226 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 26.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.058 / Rrim(I) all: 0.131 / Net I/σ(I): 10 / Num. measured all: 203506 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G76 Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.158
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Displacement parameters | Biso max: 133.51 Å2 / Biso mean: 37.65 Å2 / Biso min: 10.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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