Structure of PDB 5yjj Chain B Binding Site BS01

Receptor Information
>5yjj Chain B (length=442) Species: 176280 (Staphylococcus epidermidis ATCC 12228) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVFKTEWAGRSLTIETGQLAKQANGAVLVRYGDTVVLSTATASKEPRFF
PLTVNYEEKMYAADEATLTARLIDRPIRPLFPKGYRHDVQIMNIVLSADP
DCSPEMAAMIGSSMALSVSDIPFQGPIAGVNVGYIDGKYVINPSVADKEI
SRLDLEVAGHKDAVNMVEAGASEITESEMLEAIFFGHEEIKRLVAFQQEI
IDHIQPIKQVYAILNDLIKEEVRRLIADEKIRPDGRKVDEIRPLESEVGL
LPRAHGSGLFTRGQTQALSVLTLGARFMHHYNFPNFSVGETGPVRAPGRR
EIGHGALGERALRYIIPDTQDFPYTIRIVSEVLESNGSSSQASICGSTLA
LMDAGVPIKAPVAGIAMGLVTRDDSYTILTDIQGMEDALGDMDFKVAGTK
DGITAIQMDIKIDGLTREVIEEALEQARQGRLAIMDHMLHTI
Ligand information
Ligand IDPO4
InChIInChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
InChIKeyNBIIXXVUZAFLBC-UHFFFAOYSA-K
SMILES
SoftwareSMILES
CACTVS 3.341[O-][P]([O-])([O-])=O
ACDLabs 10.04[O-]P([O-])([O-])=O
OpenEye OEToolkits 1.5.0[O-]P(=O)([O-])[O-]
FormulaO4 P
NamePHOSPHATE ION
ChEMBL
DrugBankDB14523
ZINC
PDB chain5yjj Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yjj Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R403 H407 S441 S442 S443 K498
Binding residue
(residue number reindexed from 1)		R300 H304 S338 S339 S340 K395
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.8: polyribonucleotide nucleotidyltransferase.
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004654 polyribonucleotide nucleotidyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006396 RNA processing
GO:0006401 RNA catabolic process
GO:0006402 mRNA catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yjj, PDBe:5yjj, PDBj:5yjj
PDBsum5yjj
PubMed29242153
UniProtQ8CST1|PNP_STAES Polyribonucleotide nucleotidyltransferase (Gene Name=pnp)

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