Structure of PDB 4i9q Chain B

Receptor sequence

>4i9qB (length=873) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGALGNVWFRY
YDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYV
SADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNK
QHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWAMEGTRYAEPKLKI
MGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYI
SIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEG
EKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFI
KPLEGFTSAAKLDYEKKASLFDM

3D structure

• PDB: 4i9q 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: 2.3 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 D275 F359 S360 P361 I362 Y391 P392 G393 V396 L561 S565 G568 N572 K705 K706 R707 S784 N786 P799 K800 F803 K874	I253 N255 Y257 R260 D275 F359 S360 P361 I362 Y391 P392 G393 V396 L534 S538 G541 N545 K678 K679 R680 S757 N759 P772 K773 F776 K847
BS02	dna	B	N284 D621 D623 M728 G729 Q733 S735 S784 N786 Y791 H804	N284 D594 D596 M701 G702 Q706 S708 S757 N759 Y764 H777
BS03	XG4	B	S414 L415 Y416 R482 K560 N564	S414 L415 Y416 R482 K533 N537
BS04	XG4	B	S36 F38 K48 Y49 R59 M85 D95 F370 K374 K378 I380	S36 F38 K48 Y49 R59 M85 D95 F370 K374 K378 I380
BS05	CA	B	D411 L412	D411 L412

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:4i9q, PDBe:4i9q, PDBj:4i9q
• PDBsum: 4i9q
• PubMed: 24116139
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)