Structure of PDB 4khn Chain A Binding Site BS03

Receptor Information
>4khn Chain A (length=901) 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
AGMTAQINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWAMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
F
Ligand information
Ligand IDXG4
InChIInChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
InChIKeyDWGAAFQEGIMTIA-KVQBGUIXSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.7.0c1nc2c(n1C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
FormulaC10 H17 N6 O12 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
ChEMBL
DrugBank
ZINCZINC000032016794
PDB chain4khn Chain A Residue 1001 [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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PDB4khn A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		S36 F38 Y49 R59 G84 M85 D95 F370 K374 K378 V379 I380
Binding residue
(residue number reindexed from 1)		S36 F38 Y49 R59 G84 M85 D95 F370 K374 K378 V379 I380
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:4khn, PDBe:4khn, PDBj:4khn
PDBsum4khn
PubMed24116139
UniProtQ38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)

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