Structure of PDB 4khu Chain A

Receptor sequence

>4khuA (length=898) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIESREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLK
YDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQ
IQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRY
KYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVY
SCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALH
NPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMT
AQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEY
LNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKF
ARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTG
KKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQ
EGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFH
IRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEI
TDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD

3D structure

• PDB: 4khu Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
• Chain: A
• Resolution: 2.05 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 Y567 G568 N572 W574 K705 K706 R707 K800 K844 K874	S356 P357 I358 Y387 P388 G389 A390 S561 Y563 G564 N568 W570 K701 K702 R703 K796 K840 K870
BS02	dna	A	N284 K706 Y708 M728 G729 K734 S735 S783 S784 K790 Y791 H804	N280 K702 Y704 M724 G725 K730 S731 S779 S780 K786 Y787 H800
BS03	TTP	A	D411 S414 F415 Y416 R482 K560 N564 D623	D407 S410 F411 Y412 R478 K556 N560 D619
BS04	CA	A	D411 L412 D623	D407 L408 D619
BS05	CA	A	N505 N507 K531	N501 N503 K527
BS06	CA	A	D192 E196	D192 E196

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:4khu, PDBe:4khu, PDBj:4khu
• PDBsum: 4khu
• PubMed: 24082122
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)