Structure of PDB 5d49 Chain A

Receptor sequence

>5d49A (length=356) Species: 10090 (Mus musculus)

KKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSV
LKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYK
SFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYE
DLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFL
ITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDA
LDHFQKCFLILKLDHGRVHEGKGWKAIRVDLVMCPYDRRAFALLGWTGSR
QFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIE
PWERNA

3D structure

• PDB: 5d49 Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.
• Chain: A
• Resolution: 1.99 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D343 D345 D434
• Catalytic site (residue number reindexed from 1): D196 D198 D280
• 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	T286 Q287 I380 L381 E382 T384 D396	T139 Q140 I233 L234 E235 T237 D249
BS02	dna	A	F256 G257 V258 G259 K261 T262 M288 D343 D345 D396 L398 F405 R432 D434 G449 W450 G452 R454 E457	F109 G110 V111 G112 K114 T115 M141 D196 D198 D249 L251 F258 R278 D280 G295 W296 G298 R300 E303
BS03	dna	A	L189 R393 A397 R454 R458 R461 R462 T465 H466 M471	L42 R246 A250 R300 R304 R307 R308 T311 H312 M317
BS04	dna	A	G186 S187 A190 C216 G218 K220 V221	G39 S40 A43 C69 G71 K73 V74
BS05	MG	A	D343 D345	D196 D198

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:5d49, PDBe:5d49, PDBj:5d49
• PDBsum: 5d49
• PubMed: 27499438
• UniProt: P09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)