Structure of PDB 1q9x Chain D Binding Site BS04

Receptor Information
>1q9x Chain D (length=903) 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
EALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEV
AGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
FDF
Ligand information
Ligand ID3DR
InChIInChI=1S/C5H11O6P/c6-4-1-2-10-5(4)3-11-12(7,8)9/h4-6H,1-3H2,(H2,7,8,9)/t4-,5+/m0/s1
InChIKeyBVOBPNSQIRMLCA-CRCLSJGQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OCC1OCCC1O)(O)O
OpenEye OEToolkits 1.5.0C1CO[C@@H]([C@H]1O)COP(=O)(O)O
CACTVS 3.341O[C@H]1CCO[C@@H]1CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C1COC(C1O)COP(=O)(O)O
CACTVS 3.341O[CH]1CCO[CH]1CO[P](O)(O)=O
FormulaC5 H11 O6 P
Name1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE;
ABASIC DIDEOXYRIBOSE
ChEMBL
DrugBank
ZINCZINC000005848245
PDB chain1q9x Chain H Residue 912 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1q9x Lesion (in)tolerance reveals insights into DNA replication fidelity.
Resolution2.69 Å
Binding residue
(original residue number in PDB)		S360 P361 I362
Binding residue
(residue number reindexed from 1)		S360 P361 I362
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1q9x, PDBe:1q9x, PDBj:1q9x
PDBsum1q9x
PubMed15057282
UniProtQ38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)

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