- PDB-3zo5: Structure of SENP2-Loop1 in complex with preSUMO-2 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3zo5
Title
Structure of SENP2-Loop1 in complex with preSUMO-2
Components
SENTRIN-SPECIFIC PROTEASE 2
SMALL UBIQUITIN-RELATED MODIFIER 2
Keywords
HYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information
SUMO-specific endopeptidase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / regulation of Wnt signaling pathway / SUMOylation of RNA binding proteins ...SUMO-specific endopeptidase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / regulation of Wnt signaling pathway / SUMOylation of RNA binding proteins / fat cell differentiation / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / negative regulation of protein ubiquitination / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein ubiquitination / protein destabilization / SUMOylation of intracellular receptors / PML body / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Processing of DNA double-strand break ends / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / ubiquitin protein ligase binding / proteolysis / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function
Mass: 27797.127 Da / Num. of mol.: 1 / Fragment: RESIDUES 363-589 / Mutation: YES Source method: isolated from a genetically manipulated source Details: INSERTION OF PPPPAKGG INSTEAD OF F393 AND K394 FROM THE SENP2 NUMBERING Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HC62, Ulp1 peptidase
Resolution: 2.15→80.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.509 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSERTION OF PPPPAKGG INSTEAD OF F393 AND K394 FROM THE SENP2 NUMBERING
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23627
1193
5.1 %
RANDOM
Rwork
0.18814
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obs
0.19041
22034
99.73 %
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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