Structure of PDB 2p5o Chain C

Receptor sequence

>2p5oC (length=853) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNMLFRA
QRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQ
WIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTN
HWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGS
KGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKAL
KECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGG
FPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKC
IAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKA
SLF

3D structure

• PDB: 2p5o Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
• Chain: C
• Resolution: 2.8 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	C	E219 I253 N255 D275 F359 S360 P361 I362 G393 G568 N572 K705 R707 K800 F803 K844 K874	E219 I253 N255 D275 F359 S360 P361 I362 G393 G523 N527 K660 R662 K755 F758 K799 K829
BS02	dna	C	N284 D623 M728 G729 Q733 K734 S735 S783 S784 N786 Y791 P802 H804	N284 D578 M683 G684 Q688 K689 S690 S738 S739 N741 Y746 P757 H759

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:2p5o, PDBe:2p5o, PDBj:2p5o
• PDBsum: 2p5o
• PubMed: 15057283
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)