Structure of PDB 4khn Chain B

Receptor sequence

>4khnB (length=870) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGALGNVWFRYYDLR
NATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADK
IIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLM
FMDREAIAGPPLGSKGIGGFWTGKKRYALNVWAMEGTRYAEPKLKIMGLE
TQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIAS
VSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVY
VLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLE
GFTSAAKLDYEKKASLFDMF

3D structure

• PDB: 4khn A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site.
• Chain: B
• Resolution: 2.55 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	B	I253 N255 Y257 R260 F359 S360 P361 I362 Y391 P392 G393 A394 S565 G568 N572 K705 R707 S784 N786 K800 F803	I253 N255 Y257 R260 F359 S360 P361 I362 Y391 P392 G393 A394 S534 G537 N541 K674 R676 S753 N755 K769 F772
BS02	dna	B	N284 D621 T622 D623 K706 Y708 M728 G729 Q733 K734 S735 S784 N786 K790 Y791 H804	N284 D590 T591 D592 K675 Y677 M697 G698 Q702 K703 S704 S753 N755 K759 Y760 H773
BS03	XG4	B	S36 F38 Y49 G84 M85 D95 F370 K374 V379 I380	S36 F38 Y49 G84 M85 D95 F370 K374 V379 I380
BS04	XG4	B	L415 Y416 K560 N564 T622 D623	L415 Y416 K529 N533 T591 D592

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:4khn, PDBe:4khn, PDBj:4khn
• PDBsum: 4khn
• PubMed: 24116139
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)