Structure of PDB 1q9x Chain D Binding Site BS05

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 IDDOC
InChIInChI=1S/C9H14N3O6P/c10-7-3-4-12(9(13)11-7)8-2-1-6(18-8)5-17-19(14,15)16/h3-4,6,8H,1-2,5H2,(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1
InChIKeyRAJMXAZJKUGYGW-POYBYMJQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=NC2=O)N
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(O)=O)O2
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0C1CC(OC1COP(=O)(O)O)N2C=CC(=NC2=O)N
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(CC2)COP(=O)(O)O
FormulaC9 H14 N3 O6 P
Name2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL1232305
DrugBankDB02883
ZINCZINC000001611080
PDB chain1q9x Chain L Residue 953 [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)		T622 Y708
Binding residue
(residue number reindexed from 1)		T622 Y708
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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