Structure of PDB 4khy Chain A

Receptor sequence

>4khyA (length=899) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKL
KYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKI
QIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNR
YKYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDV
YSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEAL
HNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGM
TAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNE
YLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDK
FARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWT
GKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRML
QEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPF
HIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTE
ITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD

3D structure

• PDB: 4khy Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
• Chain: A
• Resolution: 2.25 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 L561 N564 S565 G568 N572 W574 K705 K706 R707 K800 K844 K874	S357 P358 I359 Y388 P389 G390 A391 L558 N561 S562 G565 N569 W571 K702 K703 R704 K797 K841 K871
BS02	dna	A	N284 D621 T622 K706 M728 G729 K734 S735 S783 S784 N786 Y791 K800 H804	N281 D618 T619 K703 M725 G726 K731 S732 S780 S781 N783 Y788 K797 H801
BS03	TTP	A	D411 L412 S414 F415 Y416 R482 K560 D623	D408 L409 S411 F412 Y413 R479 K557 D620
BS04	CA	A	D411 L412 D623	D408 L409 D620
BS05	CA	A	E660 D684	E657 D681
BS06	CA	A	D192 E196	D192 E196
BS07	CA	A	N505 N507 K531 K532	N502 N504 K528 K529

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