Structure of PDB 4khs Chain A

Receptor sequence

>4khsA (length=893) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
REIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPI
SKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF
SPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMS
FDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPN
GMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS
VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINR
KLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVC
GTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERM
EPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYA
LNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEES
LQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGIL
TYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIK
DDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD

3D structure

• PDB: 4khs Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
• Chain: A
• Resolution: 2.12 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	N284 D621 M728 G729 K734 S735 S783 S784 N786 Y791 H804	N275 D612 M719 G720 K725 S726 S774 S775 N777 Y782 H795
BS02	dna	A	S360 P361 I362 Y391 P392 G393 A394 S565 G568 A569 N572 W574 K705 K706 R707 K800 C801 K844 K874	S351 P352 I353 Y382 P383 G384 A385 S556 G559 A560 N563 W565 K696 K697 R698 K791 C792 K835 K865
BS03	CA	A	D411 L412 D623	D402 L403 D614
BS04	TTP	A	D411 S414 F415 Y416 R482 K560 N564 D623	D402 S405 F406 Y407 R473 K551 N555 D614
BS05	CA	A	D192 E196	D192 E196
BS06	CA	A	N505 N507 K531 K532	N496 N498 K522 K523

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