- PDB-6go4: TdT chimera (Loop1 of pol mu) - binary complex with ddCTP -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 6go4
Title
TdT chimera (Loop1 of pol mu) - binary complex with ddCTP
Components
DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
Keywords
DNA BINDING PROTEIN / NHEJ pathway / DNA bridging / DNA polymerase polX
Function / homology
Function and homology information
DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function
DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Polymerase, nucleotidyl transferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Nucleotidyltransferase domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain ...DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Polymerase, nucleotidyl transferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Nucleotidyltransferase domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA nucleotidylexotransferase / DNA-directed DNA/RNA polymerase mu Similarity search - Component
DNAnucleotidylexotransferase,DNA-directedDNA/RNApolymerasemu,DNAnucleotidylexotransferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase / Pol Mu / ...Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase / Pol Mu / Terminal transferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase
Mass: 45848.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol ...Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt, Polm, polmu / Production host: Escherichia coli (E. coli) References: UniProt: P09838, UniProt: Q9JIW4, DNA nucleotidylexotransferase, DNA-directed DNA polymerase
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi