Structure of PDB 5d46 Chain A Binding Site BS06

Receptor Information

>5d46 Chain A (length=346) Species: 10090 (Mus musculus)

KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVL
KSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKS
FKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYED
LVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLI
TSPATEDEEQQLLHKVTDFWKQQGLLLYCDILESPSRKVDALDHFQKCFL
ILKLDHGRVHGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYA
THERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 5d46 Chain A Residue 603

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d46 Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): G332 G333 R336 H342
• Binding residue (residue number reindexed from 1): G184 G185 R188 H194
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): D343 D345 D434
• Catalytic site (residue number reindexed from 1): D195 D197 D270
• Enzyme Commision number: 2.7.7.31: DNA nucleotidylexotransferase.
  3.1.11.-

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:5d46, PDBe:5d46, PDBj:5d46
• PDBsum: 5d46
• PubMed: 27499438
• UniProt: P09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)