Structure of PDB 4khs Chain A Binding Site BS04

Receptor Information
>4khs Chain A (length=893) 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
REIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPI
SKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVF
SPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMS
FDLTSFYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPN
GMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLS
VDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINR
KLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVC
GTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERM
EPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYA
LNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEES
LQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGIL
TYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIK
DDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD
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 chain4khs Chain A Residue 1002 [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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PDB4khs Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Resolution2.12 Å
Binding residue
(original residue number in PDB)		D411 S414 F415 Y416 R482 K560 N564 D623
Binding residue
(residue number reindexed from 1)		D402 S405 F406 Y407 R473 K551 N555 D614
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:4khs, PDBe:4khs, PDBj:4khs
PDBsum4khs
PubMed24082122
UniProtQ38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)

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