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Yorodumi- PDB-4nzm: Crystal structure of the catalytic domain of PPIP5K2 in complex w... -
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-Basic information
Entry | Database: PDB / ID: 4nzm | ||||||
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Title | Crystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 5-PA-InsP5 | ||||||
Components | Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ATP-grasp Fold / Inositol Pyrophosphate Kinase / drug discovery / kinase / enzymology / inositol pyrophosphates / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process ...diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / Synthesis of pyrophosphates in the cytosol / inositol hexakisphosphate kinase activity / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / sensory perception of sound / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Wang, H. / Shears, S.B. | ||||||
Citation | Journal: Chem.Biol. / Year: 2014 Title: Synthetic Inositol Phosphate Analogs Reveal that PPIP5K2 Has a Surface-Mounted Substrate Capture Site that Is a Target for Drug Discovery. Authors: Wang, H. / Godage, H.Y. / Riley, A.M. / Weaver, J.D. / Shears, S.B. / Potter, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nzm.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nzm.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nzm_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4nzm_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4nzm_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 4nzm_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/4nzm ftp://data.pdbj.org/pub/pdb/validation_reports/nz/4nzm | HTTPS FTP |
-Related structure data
Related structure data | 4nznC 4nzoC 3t9bS 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: 37568.891 Da / Num. of mol.: 1 / Fragment: ATP-grasp Kinase domain, UNP residues 41-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIP5K2, HISPPD1, KIAA0433, VIP2 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express (DE3) References: UniProt: O43314, inositol-hexakisphosphate 5-kinase, diphosphoinositol-pentakisphosphate 1-kinase | ||
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#2: Chemical | ChemComp-ANP / | ||
#3: Chemical | ChemComp-0EJ / ( | ||
#4: Chemical | ChemComp-MG / #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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP with 2 mM CdCl2 Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M Sodium Acetate, pH5.2 with 10 mM 5PA-InsP5, 3 days, VAPOR ...Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP with 2 mM CdCl2 Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M Sodium Acetate, pH5.2 with 10 mM 5PA-InsP5, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 28028 / Num. obs: 28028 / % possible obs: 97.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.114 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1307 / Rsym value: 0.511 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3T9B Resolution: 2→34.28 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 23.063 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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