Structure of PDB 5lkm Chain B Binding Site BS01

Receptor Information
>5lkm Chain B (length=346) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPMKLAEVTNRTKTEMEEFNRVLGGGVVPGSLVLIGGDPGIGKSTLLLQ
VSTQLLYVSGEESAQQIKLRAERLSEFYLNMQSVRAEVERIQPDFLIIDS
IQGSVSQVREVTAELMQLAKTNNIAIFIVGHVLYFEGFRILRAVKNRFGS
TNEIGIFEMQSGGLVEVLNPSQVFLEERLDGATGSSIVVTMEGTRPILAE
VQALVTPTMFGNAKRTTTGLDFNRASLIMAVLEKRAGLLLQNQDAYLKSA
GGVKLDEPAIDLAVAVAIASSYKDKPTNPQECFVGELGLTGEIRRVNRIE
QRINEAAKLGFTKIYVPKNSLTGITLPKEIQVIGVTTIQEVLKKVF
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-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)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain5lkm Chain B Residue 500 [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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PDB5lkm Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		G98 G100 K101 S102 T103 R133
Binding residue
(residue number reindexed from 1)		G41 G43 K44 S45 T46 R70
Annotation score2
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0000725 recombinational repair
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5lkm, PDBe:5lkm, PDBj:5lkm
PDBsum5lkm
PubMed28561029
UniProtQ8DRP0|RADA_STRR6 DNA repair protein RadA (Gene Name=radA)

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