Structure of PDB 6kij Chain B Binding Site BS02

Receptor Information
>6kij Chain B (length=226) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CGRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERD
EHLHLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFAD
GWFEWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAA
ADQGLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSW
HPVSRAVGNVKNQGAELIQPVLEVLF
Ligand information
Ligand IDPED
InChIInChI=1S/C5H13O6P/c1-2-4(6)5(7)3-11-12(8,9)10/h4-7H,2-3H2,1H3,(H2,8,9,10)/t4-,5+/m0/s1
InChIKeyFQKLTSRHTQGSQZ-CRCLSJGQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[C@H](O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.7.5CCC(C(COP(=O)(O)O)O)O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)CC
OpenEye OEToolkits 1.7.5CC[C@@H]([C@@H](COP(=O)(O)O)O)O
CACTVS 3.385CC[CH](O)[CH](O)CO[P](O)(O)=O
FormulaC5 H13 O6 P
NamePENTANE-3,4-DIOL-5-PHOSPHATE;
OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000015614168
PDB chain6kij Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6kij Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		C2 N75 R77 T149 H160 R162
Binding residue
(residue number reindexed from 1)		C1 N74 R76 T148 H159 R161
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.-.-
4.-.-.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0008233 peptidase activity
GO:0016829 lyase activity
GO:0160129 protein-DNA covalent cross-linking activity
Biological Process
GO:0006508 proteolysis
GO:0006974 DNA damage response
GO:0009432 SOS response
GO:0106300 protein-DNA covalent cross-linking repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6kij, PDBe:6kij, PDBj:6kij
PDBsum6kij
PubMed31504793
UniProtP76318|YEDK_ECOLI Abasic site processing protein YedK (Gene Name=yedK)

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