Structure of PDB 4khw Chain A

Receptor sequence

>4khwA (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: 4khw Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
• Chain: A
• Resolution: 2.371 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 N564 S565 G568 G571 N572 W574 K705 K706 R707 K800 F803 K844 K874	S356 P357 I358 Y387 P388 G389 A390 N560 S561 G564 G567 N568 W570 K701 K702 R703 K796 F799 K840 K870
BS02	dna	A	N284 T622 K706 Y708 M728 G729 K734 S735 S783 S784 N786 Y791 H804	N280 T618 K702 Y704 M724 G725 K730 S731 S779 S780 N782 Y787 H800
BS03	TTP	A	D411 T413 S414 F415 Y416 R482 K560 D623	D407 T409 S410 F411 Y412 R478 K556 D619
BS04	CA	A	D411 L412 D623	D407 L408 D619
BS05	CA	A	D411 D623	D407 D619
BS06	CA	A	E660 D684	E656 D680
BS07	CA	A	N505 N507 K531	N501 N503 K527
BS08	CA	A	D192 E196	D192 E196
BS09	CA	A	E172 E177	E172 E177
BS10	CA	A	D411 E686 E716	D407 E682 E712

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