Structure of PDB 2p5o Chain A

Receptor sequence

>2p5oA (length=856) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRMLFRAQ
RTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQW
IERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNH
WVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSK
GIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALK
ECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGF
PGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCI
AWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKAS
LFDMFD

3D structure

• PDB: 2p5o Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
• Chain: A
• 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	A	K251 I253 D275 F359 S360 P361 I362 G393 A394 V396 G568 N572 K705 K706 R707 K800 K844 K874	K251 I253 D275 F359 S360 P361 I362 G393 A394 V396 G522 N526 K659 K660 R661 K754 K798 K828
BS02	dna	A	M728 Q733 K734 S735 S784 N786 K790 Y791 H804	M682 Q687 K688 S689 S738 N740 K744 Y745 H758
BS03	dna	A	S36 F38 K48 Y49 R59 G84 M85 D95 F370 K374 K378 V379 I380	S36 F38 K48 Y49 R59 G84 M85 D95 F370 K374 K378 V379 I380

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)