Structure of PDB 5ddy Chain A Binding Site BS01

Receptor Information

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

ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQE
ACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKT
AQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQT
VQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSE
FACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPG
RVLPTPTEKDVFRLLGLPYREPAERDW

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: 5ddy Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ddy Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda
• Resolution: 3.36 Å
• Binding residue (original residue number in PDB): D427 D429
• Binding residue (residue number reindexed from 1): D179 D181
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D179 D181 D242
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  4.2.99.-

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:5ddy, PDBe:5ddy, PDBj:5ddy
• PDBsum: 5ddy
• PubMed: 26836966
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)