Structure of PDB 6t66 Chain E Binding Site BS01

Receptor Information
>6t66 Chain E (length=440) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVPPHSLEAEQSVIGGLLLDNERWDTVSEHVMTQDFYSRPHRLIFDGVKS
ILEAGKPLDLITLSEYLEQREQLEDVGGFAYLADLAKNTPSAANINAYAE
IVAERALVRNLIGVANEIADAGYDPQGRNAEDLLDLAESKVFAIAEARTS
ENEGPKNVDSILERTLERIELLYKTPQDGVTGVNTGFTDLNKKTAGLQGS
DLIIVAARPSMGKTTFAMNLCENAAMEQDKPVLIFSLEMPAEQIMMRMLA
SLSRVDQTKIRTGQLDDEDWARISSTMGILMEKKNMYIDDSSGLTPTEVR
SRARRIAREHGGLSLIMVDYLQLMRVPALTDNRTLEIAEISRSLKALAKE
LNVPVVALSQLNRSLEQRADKRPVNSDLRESGSIEQDADLIMFIYRDEVY
HPDSPLKGTAEIIIGKQRNGPIGSVRLTFQGHYSRFDNYA
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain6t66 Chain E Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6t66 Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		S231 G233 K234 T235 T236 R268 Q278 G452
Binding residue
(residue number reindexed from 1)		S210 G212 K213 T214 T215 R247 Q257 G431
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006268 DNA unwinding involved in DNA replication
GO:0006269 DNA replication, synthesis of primer
Cellular Component
GO:0005829 cytosol
GO:1990077 primosome complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6t66, PDBe:6t66, PDBj:6t66
PDBsum6t66
PubMed34107018
UniProtQ9KUY7

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