Structure of PDB 6ppk Chain W Binding Site BS02

Receptor Information
>6ppk Chain W (length=252) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WFPGHMAKARREVTEKLKLIDIVYELVDARIPMSSRNPMIEDILKNKPRI
MLLNKADAAVTQQWKEHFENQGIRSLSINSVNGQGLNQIVPASKEILQEK
FDRMPRAIRALIIGIPNVGKSTLINRLAKKNIAKTGDRPGITTLELLDTP
GILWPKFVGLRLAVTGAIKDSIINLQDVAVFGLRFLEEHYPERLKERYGL
DEIPEDIAELFDAIGEKRGCLMSGGLINYDKTTEVIIRDIRTEKFGRLSF
EQ
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain6ppk Chain W Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ppk Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.
Resolution4.4 Å
Binding residue
(original residue number in PDB)		N58 K59 S87 P129 N130 G132 K133 S134 T135 T148 P152 G153
Binding residue
(residue number reindexed from 1)		N54 K55 S80 P116 N117 G119 K120 S121 T122 T135 P139 G140
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
Biological Process
GO:0006412 translation
GO:0042254 ribosome biogenesis
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:6ppk, PDBe:6ppk, PDBj:6ppk
PDBsum6ppk
PubMed31665744
UniProtO31743|RBGA_BACSU Ribosome biogenesis GTPase A (Gene Name=rbgA)

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