Structure of PDB 5tyv Chain A Binding Site BS07

Receptor Information

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

WMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVL
KALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQT
MKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDL
STPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLIT
HPKEGQEAGLLPRVMCRLQDQGLILYHQAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 5tyv Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5tyv Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
• Resolution: 1.93 Å
• Binding residue (original residue number in PDB): E386 H459
• Binding residue (residue number reindexed from 1): E231 H292
• 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:5tyv, PDBe:5tyv, PDBj:5tyv
• PDBsum: 5tyv
• PubMed: 28811466
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)