Structure of PDB 7f4y Chain B

Receptor sequence

>7f4yB (length=901) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEV
AGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
F

3D structure

• PDB: 7f4y Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69.
• Chain: B
• Resolution: 2.2 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  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	B	D13 R66 K247	D13 R66 K247
BS02	dna	B	E219 I253 N255 Y257 R260 F359 S360 P361 I362 Y391 P392 G393 A394 G568 G571 N572 K705 K706 R707 N786 K800 F803 K844 K874	E219 I253 N255 Y257 R260 F359 S360 P361 I362 Y391 P392 G393 A394 G568 G571 N572 K705 K706 R707 N786 K800 F803 K844 K874
BS03	dna	B	N284 D621 T622 D623 K706 Y708 M728 G729 S735 S783 S784 N786 K790 Y791 H804	N284 D621 T622 D623 K706 Y708 M728 G729 S735 S783 S784 N786 K790 Y791 H804
BS04	5GP	B	S36 F38 Y49 G84 M85 A91 D95 F370 K374 K378 V379 I380	S36 F38 Y49 G84 M85 A91 D95 F370 K374 K378 V379 I380

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004527 exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0039686 bidirectional double-stranded viral DNA replication
• GO:0039693 viral DNA genome replication

External links

• PDB: RCSB:7f4y, PDBe:7f4y, PDBj:7f4y
• PDBsum: 7f4y
• PubMed: 34869578
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)