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- PDB-5n53: Crystal structure of human 3-phosphoglycerate dehydrogenase in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n53 | ||||||
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Title | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide | ||||||
![]() | D-3-phosphoglycerate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / dehydrogenase / serine metabolism / FBDD | ||||||
Function / homology | ![]() 2-oxoglutarate reductase / threonine metabolic process / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process ...2-oxoglutarate reductase / threonine metabolic process / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / neural tube development / G1 to G0 transition / spinal cord development / glutamine metabolic process / brain development / NAD binding / neuron projection development / regulation of gene expression / electron transfer activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Unterlass, J.E. / Basle, A. / Blackburn, T.J. / Tucker, J. / Cano, C. / Noble, M.E.M. / Curtin, N.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Validating and enabling phosphoglycerate dehydrogenase (PHGDH) as a target for fragment-based drug discovery in PHGDH-amplified breast cancer. Authors: Unterlass, J.E. / Basle, A. / Blackburn, T.J. / Tucker, J. / Cano, C. / Noble, M.E.M. / Curtin, N.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.7 KB | Display | ![]() |
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PDB format | ![]() | 140.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nzoC ![]() 5nzpC ![]() 5nzqC ![]() 5ofvC ![]() 5ofwC ![]() 2g76S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 100 - 294 / Label seq-ID: 1 - 195
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Components
#1: Protein | Mass: 20952.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M PCTP, pH 7, 23-25 % PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50.12 Å / Num. obs: 51238 / % possible obs: 86.1 % / Redundancy: 2.13 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.1 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.14 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2530 / CC1/2: 0.355 / Rpim(I) all: 0.972 / % possible all: 85.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G76 Resolution: 1.48→50.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.83 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.102 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.98 Å2 / Biso mean: 19.681 Å2 / Biso min: 7.5 Å2
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Refinement step | Cycle: final / Resolution: 1.48→50.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 23386 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.484→1.522 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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