Structure of PDB 3pml Chain B Binding Site BS06

Receptor Information

>3pml Chain B (length=324) Species: 9606 (Homo sapiens)

QKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSY
QEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGT
KTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIE
QTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSR
LLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFAC
ALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVL
PTPTEKDVFRLLGLPYREPAERDW

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: 3pml Chain B Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pml Replication infidelity via a mismatch with Watson-Crick geometry.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): D427 D429
• Binding residue (residue number reindexed from 1): D181 D183
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D181 D183 D239
• 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:3pml, PDBe:3pml, PDBj:3pml
• PDBsum: 3pml
• PubMed: 21233421
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)