Structure of PDB 5tyf Chain A Binding Site BS04

Receptor Information

>5tyf Chain A (length=327) Species: 9606 (Homo sapiens)

WMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVL
KALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQT
MKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDL
STPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLIT
HPKEGQEAGLLPRVMCRLQDQGLILYHQAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA

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: 5tyf Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5tyf Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
• Resolution: 1.971 Å
• Binding residue (original residue number in PDB): D330 D332
• Binding residue (residue number reindexed from 1): D194 D196
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D330 D332 D418
• Catalytic site (residue number reindexed from 1): D194 D196 D251
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

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

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5tyf, PDBe:5tyf, PDBj:5tyf
• PDBsum: 5tyf
• PubMed: 28811466
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)