+Open data
-Basic information
Entry | Database: PDB / ID: 1kpe | ||||||
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Title | PKCI-TRANSITION STATE ANALOG | ||||||
Components | PROTEIN KINASE C INTERACTING PROTEIN | ||||||
Keywords | PROTEIN KINASE INHIBITOR / PKCI-1 / HIT PROTEIN FAMILY / HISTIDINE TRIAD PROTEIN FAMILY / NUCLEOTIDYL HYDROLASE / NUCLEOTIDYL TRANSFERASE / PENTACOVALENT NUCLEOTIDYL HISTIDYL-TUNGSTATE COMPLEX | ||||||
Function / homology | Function and homology information purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Lima, C.D. / Klein, M.G. / Hendrickson, W.A. | ||||||
Citation | Journal: Science / Year: 1997 Title: Structure-based analysis of catalysis and substrate definition in the HIT protein family. Authors: Lima, C.D. / Klein, M.G. / Hendrickson, W.A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Three-Dimensional Structure of Human Protein Kinase C Interacting Protein 1, a Member of the Hit Family of Proteins Authors: Lima, C.D. / Klein, M.G. / Weinstein, I.B. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kpe.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kpe.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kpe_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 1kpe_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 1kpe_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1kpe_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/1kpe ftp://data.pdbj.org/pub/pdb/validation_reports/kp/1kpe | HTTPS FTP |
-Related 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: 13718.772 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPKCI-1 / Plasmid: PHIL-D5 / Gene (production host): HPKCI-1 / Production host: Pichia pastoris (fungus) / References: UniProt: P49773 #2: Chemical | ChemComp-ADW / | #3: Water | ChemComp-HOH / | Compound details | THE NUCLEOTIDYLATED PROTEIN STRUCTURE REPORTED HERE REPRESENTS A PENTACOVALENT TRANSITION STATE ...THE NUCLEOTIDY | |
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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: 2.65 Å3/Da / Density % sol: 53.5 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: GROWN FROM PEG8K PH6.5 THE PENTACOVALENT TRANSITION STATE ANALOG WAS PREPARED BY SOAKING SODIUM TUNGSTATE AND ADENOSINE INTO THE CRYSTAL. THE COMPOUNDS WERE FOUND TO BIND IN THE ACTIVE SITE ...Details: GROWN FROM PEG8K PH6.5 THE PENTACOVALENT TRANSITION STATE ANALOG WAS PREPARED BY SOAKING SODIUM TUNGSTATE AND ADENOSINE INTO THE CRYSTAL. THE COMPOUNDS WERE FOUND TO BIND IN THE ACTIVE SITE OF CHAIN B. THE ACTIVE SITE OF CHAIN A IS BLOCKED BY A LATTICE CONTACT AND IS NOT AVAILABLE TO THE SUBSTRATE. THREE NEW BONDS ARE FORMED UPON SOAKING THIS MIXTURE INTO THE PKCI CRYSTALS: ONE BETWEEN THE NE OF HIS B 112 AND THE ALPHA TUNGSTATE, ONE BETWEEN THE ALPHA AND BETA TUNGSTATE IONS, AND ONE BETWEEN THE NUCLEOSIDE RIBOSE AND THE ALPHA TUNGSTATE ION. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: Lima, C.D., (1996) Proc.Nat.Acad.Sci.USA, 93, 5357. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 10, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 23339 / % possible obs: 84.3 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.085 |
Reflection | *PLUS Num. obs: 43312 / Num. measured all: 318416 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2 Details: REFINED ADW WITH GEOMETRY SIMILAR TO THAT OF ADP WITH MODIFICATIONS TO INCLUDE A PENTACOVALENT ALPHA TUNGSTATE POSITION, THE LONGER TUNGSTATE OXYGEN BONDS, AND THE TUNGSTATE ATOMS.
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Displacement parameters | Biso mean: 22.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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