Structure of PDB 7m4a Chain A Binding Site BS04

Receptor Information

>7m4a Chain A (length=320) Species: 9606 (Homo sapiens)

NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEAC
SIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQ
MWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQ
KAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDS
LRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLY
FTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPT
EKDVFRLLGLPYREPAERDW

Ligand information

• Ligand ID: PPV
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)O
  CACTVS 3.341: O[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: OP(=O)(O)OP(=O)(O)O
• Formula: H4 O7 P2
• Name: PYROPHOSPHATE
• ChEMBL: CHEMBL1160571
• DrugBank: DB04160
• ZINC: ZINC000006827695
• PDB chain: 7m4a Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m4a Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints.
• Resolution: 1.868 Å
• Binding residue (original residue number in PDB): R386 S417 R420 C425 G426 D427 D429
• Binding residue (residue number reindexed from 1): R136 S167 R170 C175 G176 D177 D179
• Annotation score: 5

Enzymatic activity

• 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:7m4a, PDBe:7m4a, PDBj:7m4a
• PDBsum: 7m4a
• PubMed: 35680862
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)