Structure of PDB 5d4b Chain A

Receptor sequence

>5d4bA (length=350) Species: 10090 (Mus musculus)

KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVL
KSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKS
FKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYED
LVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLI
TSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKQPSRALDHFQK
CFLILKLDHGRVHEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDL
RRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA

3D structure

• PDB: 5d4b Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.
• Chain: A
• Resolution: 2.66 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D343 D345 D434
• Catalytic site (residue number reindexed from 1): D195 D197 D274
• Enzyme Commision number: 2.7.7.31: DNA nucleotidylexotransferase.
  3.1.11.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	G257 V258 G259 K261 T262 M288 D343 D345 L398 F405 R432 D434 W450 G452 R454	G109 V110 G111 K113 T114 M140 D195 D197 L245 F252 R272 D274 W290 G292 R294
BS02	dna	A	G186 R393 R462	G38 R243 R302
BS03	dna	A	G186 S187 A190 C216 G218 K220 V221	G38 S39 A42 C68 G70 K72 V73
BS04	MG	A	D343 D345	D195 D197

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:5d4b, PDBe:5d4b, PDBj:5d4b
• PDBsum: 5d4b
• PubMed: 27499438
• UniProt: P09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)