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Yorodumi- PDB-5np8: PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5np8 | ||||||
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Title | PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid) | ||||||
Components | Phosphoglycerate kinase 1 | ||||||
Keywords | TRANSFERASE / Kinase | ||||||
Function / homology | Function and homology information Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / phosphorylation / epithelial cell differentiation / negative regulation of angiogenesis / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / membrane raft / extracellular space / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Turnbull, A.P. / Bilsland, A.E. / Liu, Y. / Sumpton, D. / Stevenson, K. / Cairney, C.J. / Roffey, J. / Jenkinson, D. / Keith, W.N. | ||||||
Citation | Journal: Neoplasia / Year: 2019 Title: A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation. Authors: Bilsland, A.E. / Liu, Y. / Turnbull, A. / Sumpton, D. / Stevenson, K. / Cairney, C.J. / Boyd, S.M. / Roffey, J. / Jenkinson, D. / Keith, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5np8.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5np8.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 5np8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5np8_validation.pdf.gz | 698.4 KB | Display | wwPDB validaton report |
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Full document | 5np8_full_validation.pdf.gz | 703.5 KB | Display | |
Data in XML | 5np8_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5np8_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/5np8 ftp://data.pdbj.org/pub/pdb/validation_reports/np/5np8 | HTTPS FTP |
-Related structure data
Related structure data | 2zgvS S: Starting model for refinement |
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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: 44954.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PGK1, PGKA, MIG10, OK/SW-cl.110 / Production host: Escherichia coli (E. coli) / References: UniProt: P00558, phosphoglycerate kinase | ||||
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#2: Chemical | ChemComp-93T / | ||||
#3: Chemical | #4: Chemical | ChemComp-3PG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2.4-2.8M Sodium potassium phosphate, pH 7.4 - 8.2, 10mM DTT PH range: 7.4 - 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 28225 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.358 / Num. unique obs: 4041 / % possible all: 96.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZGV Resolution: 1.9→28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.538 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.778 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→28 Å
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Refine LS restraints |
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