Structure of PDB 2dy4 Chain B Binding Site BS01

Receptor Information
>2dy4 Chain B (length=888) Species: 12353 (Escherichia phage RB69) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
DVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLIN
SLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGE
AFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAID
RGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWD
MEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYF
KEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRA
IKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLH
WMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD
Ligand information
Receptor-Ligand Complex Structure
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PDB2dy4 A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		K279 S360 P361 I362 Y391 G393 A394 G571 N572 W574 K705 K706 R707 K800 K844
Binding residue
(residue number reindexed from 1)		K279 S360 P361 I362 Y391 G393 A394 G557 N558 W560 K691 K692 R693 K786 K830
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2dy4, PDBe:2dy4, PDBj:2dy4
PDBsum2dy4
PubMed17210917
UniProtQ38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)

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