Structure of PDB 1kdh Chain A Binding Site BS02

Receptor Information

>1kdh Chain A (length=356) Species: 10090 (Mus musculus)

KKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSV
LKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYK
SFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYE
DLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFL
ITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRLDHF
QKCFLILKLDHGRVHSEKSEGKGWKAIRVDLVMCPYDRRAFALLGWTGSR
QFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIE
PWERNA

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 1kdh Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1kdh Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D345 D434 W450
• Binding residue (residue number reindexed from 1): D198 D280 W296
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D343 D345
• Catalytic site (residue number reindexed from 1): D196 D198
• Enzyme Commision number: 2.7.7.31: DNA nucleotidylexotransferase.
  3.1.11.-

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:1kdh, PDBe:1kdh, PDBj:1kdh
• PDBsum: 1kdh
• PubMed: 11823435
• UniProt: P09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)