Structure of PDB 6gfm Chain A Binding Site BS01

Receptor Information
>6gfm Chain A (length=440) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRAITHISPLGSMDMLSQLEVDMLKRTASSDLYQLFRNCSLAVLNSGSLT
DNSKELLSRFENFDINVLRRERGVKLELINPPEEAFVDGRIIRALQANLF
AVLRDILFVYGQIHNTVRFPNLNLDNSVHITNLVFSILRNARALHVGEAP
NMVVCWGGHSINENEYLYARRVGNQLGLRELNICTGCGPGAMEAPMKGAA
VGHAQQRYKDSRFIGMTEPSIIAAEPPNPLVNELIIMPDIEKRLEAFVRI
AHGIIIFPGGVGTAEELLYLLGILMNPANKDQVLPLILTGPKESADYFRV
LDEFVVHTLGENARRHYRIIIDDAAEVARQMKKSMPLVKENRRDTGDAYS
FNWSMRIAPDLQMPFEPSHENMANLKLYPDQPVEVLAADLRRAFSGIVAG
NVKEVGIRAIEEFGPYKINGDKEIMRRMDDLLQGFVAQHR
Ligand information
Ligand ID0O2
InChIInChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyKCPMACXZAITQAX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=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[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H18 N5 O20 P5
Nameguanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
ChEMBL
DrugBank
ZINCZINC000083923877
PDB chain6gfm Chain A Residue 501 [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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PDB6gfm (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch.
Resolution2.77 Å
Binding residue
(original residue number in PDB)		R340 G343 D344 A345 Y346
Binding residue
(residue number reindexed from 1)		R343 G346 D347 A348 Y349
Annotation score2
Enzymatic activity
Enzyme Commision number 3.2.2.-
3.2.2.10: pyrimidine-5'-nucleotide nucleosidase.
3.2.2.4: AMP nucleosidase.
Gene Ontology
Molecular Function
GO:0008714 AMP nucleosidase activity
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0047405 pyrimidine-5'-nucleotide nucleosidase activity
GO:0047723 inosinate nucleosidase activity
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0051289 protein homotetramerization
Cellular Component
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6gfm, PDBe:6gfm, PDBj:6gfm
PDBsum6gfm
PubMed31023582
UniProtP0ADR8|PPNN_ECOLI Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase (Gene Name=ppnN)

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