Structure of PDB 7sp3 Chain A Binding Site BS01

Receptor Information
>7sp3 Chain A (length=153) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAM
YRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVCIGQKQKWFLLQLVSG
DAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMS
LAA
Ligand information
Ligand IDB4P
InChIInChI=1S/C20H28N10O19P4/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(45-19)1-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-2-8-12(32)14(34)20(46-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyYOAHKNVSNCMZGQ-XPWFQUROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
FormulaC20 H28 N10 O19 P4
NameBIS(ADENOSINE)-5'-TETRAPHOSPHATE
ChEMBLCHEMBL339385
DrugBank
ZINCZINC000096014967
PDB chain7sp3 Chain A Residue 201 [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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PDB7sp3 A distinct RNA recognition mechanism governs Np 4 decapping by RppH.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		R8 R27 S32 Q37 G38 E53 Y77 L79 Q95 E120 V137 K140
Binding residue
(residue number reindexed from 1)		R8 R27 S32 Q37 G38 E53 Y77 L79 Q88 E113 V130 K133
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005515 protein binding
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0034353 mRNA 5'-diphosphatase activity
GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0008033 tRNA processing
GO:0050779 RNA destabilization
GO:0110154 RNA decapping
GO:0110155 NAD-cap decapping
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7sp3, PDBe:7sp3, PDBj:7sp3
PDBsum7sp3
PubMed35131855
UniProtP0A776|RPPH_ECOLI RNA pyrophosphohydrolase (Gene Name=rppH)

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