- PDB-6f8f: Co-crystal structure of SPOP MATH domain and human Pdx1 fragment -
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Basic information
Entry
Database: PDB / ID: 6f8f
Title
Co-crystal structure of SPOP MATH domain and human Pdx1 fragment
Components
Pancreas/duodenum homeobox protein 1
Speckle-type POZ protein
Keywords
LIGASE / Nuclear / Diabetes
Function / homology
Function and homology information
: / response to vitamin / detection of glucose / type B pancreatic cell differentiation / negative regulation of type B pancreatic cell apoptotic process / transdifferentiation / : / Regulation of gene expression in early pancreatic precursor cells / response to chlorate / morphogenesis of embryonic epithelium ...: / response to vitamin / detection of glucose / type B pancreatic cell differentiation / negative regulation of type B pancreatic cell apoptotic process / transdifferentiation / : / Regulation of gene expression in early pancreatic precursor cells / response to chlorate / morphogenesis of embryonic epithelium / response to xenobiotic stimulus => GO:0009410 / chromatin => GO:0000785 / endocrine pancreas development / response to L-leucine / response to fatty acid / exocrine pancreas development / regulation of proteolysis / response to alkaloid / digestive tract development / response to iron(II) ion / insulin secretion / Cul3-RING ubiquitin ligase complex / smoothened signaling pathway / molecular function inhibitor activity / positive regulation of DNA binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Regulation of gene expression in beta cells / transcription factor binding / nitric oxide mediated signal transduction / animal organ regeneration / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / response to glucocorticoid / liver development / generation of precursor metabolites and energy / response to cytokine / central nervous system development / stem cell differentiation / promoter-specific chromatin binding / animal organ morphogenesis / Hedgehog 'on' state / response to nicotine / response to wounding / protein polyubiquitination / glucose metabolic process / sequence-specific double-stranded DNA binding / glucose homeostasis / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function
Homeobox protein, antennapedia type / SPOP, C-terminal BACK domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Homeobox domain, metazoa / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like ...Homeobox protein, antennapedia type / SPOP, C-terminal BACK domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Homeobox domain, metazoa / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Homeobox-like domain superfamily / Sandwich / Mainly Beta Similarity search - Domain/homology
Resolution: 2→19.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.211 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27433
640
5 %
RANDOM
Rwork
0.21549
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obs
0.21841
12184
99.07 %
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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