Structure of PDB 4khy Chain A Binding Site BS03

Receptor Information
>4khy Chain A (length=899) 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
KVIENSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKL
KYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKI
QIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNR
YKYVMSFDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDV
YSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEAL
HNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGM
TAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNE
YLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDK
FARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWT
GKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRML
QEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPF
HIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTE
ITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain4khy 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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PDB4khy Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		D411 L412 S414 F415 Y416 R482 K560 D623
Binding residue
(residue number reindexed from 1)		D408 L409 S411 F412 Y413 R479 K557 D620
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:4khy, PDBe:4khy, PDBj:4khy
PDBsum4khy
PubMed24082122
UniProtQ38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)

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