Structure of PDB 4du4 Chain A

Receptor sequence

>4du4A (length=902) Species: 12353 (Escherichia phage RB69)

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

3D structure

• PDB: 4du4 Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.
• Chain: A
• Resolution: 2.28 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	A	S360 P361 I362 Y391 P392 G393 A394 S565 G568 G571 N572 W574 K705 K706 R707 P799 K800 C801 F803 K844 K874	S360 P361 I362 Y391 P392 G393 A394 S565 G568 G571 N572 W574 K705 K706 R707 P799 K800 C801 F803 K844 K874	PDBbind-CN: Kd=38uM
BS02	dna	A	N284 D621 T622 K706 Y708 M728 G729 Q733 K734 S735 S783 S784 N786 H804	N284 D621 T622 K706 Y708 M728 G729 Q733 K734 S735 S783 S784 N786 H804	PDBbind-CN: Kd=38uM
BS03	DTP	A	S414 L415 Y416 R482 K560 T622 D623	S414 L415 Y416 R482 K560 T622 D623
BS04	CA	A	D411 L412 D623	D411 L412 D623
BS05	CA	A	D411 D623	D411 D623
BS06	CA	A	N505 N507 K531	N505 N507 K531
BS07	CA	A	D411 E716	D411 E716
BS08	CA	A	L857 D861	L857 D861
BS09	CA	A	E660 D684	E660 D684

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:4du4, PDBe:4du4, PDBj:4du4
• PDBsum: 4du4
• PubMed: 22571765
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)