Structure of PDB 7bl5 Chain 9 Binding Site BS02

Receptor Information
>7bl5 Chain 9 (length=338) Species: 511145 (Escherichia coli str. K-12 substr. MG1655) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEAD
ENLNTLIDYRFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQG
TGETMGDMTKHGQRLLVAKGGWHGLGNTRFKSSVNRTPRQKTNGTPGDKR
ELLLELMLLADVGMLGMPNAGKSTFIRAVSAAKPKVADYPFTTLVPSLGV
VRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRVLLHLIDIDPI
DGTDPVENARIIISELEKYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI
AEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVV
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(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)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain7bl5 Chain 9 Residue 1001 [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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PDB7bl5 Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		P168 N169 A170 G171 K172 T174 A187 D188 T192 N283 K284 D286 A316
Binding residue
(residue number reindexed from 1)		P168 N169 A170 G171 K172 T174 A187 D188 T192 N283 K284 D286 A316
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0017111 ribonucleoside triphosphate phosphatase activity
GO:0019003 GDP binding
GO:0019843 rRNA binding
GO:0032561 guanyl ribonucleotide binding
GO:0043023 ribosomal large subunit binding
GO:0046872 metal ion binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0007059 chromosome segregation
GO:0022611 dormancy process
GO:0042254 ribosome biogenesis
GO:0042255 ribosome assembly
GO:0090071 negative regulation of ribosome biogenesis
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:7bl5, PDBe:7bl5, PDBj:7bl5
PDBsum7bl5
PubMed33639093
UniProtP42641|OBG_ECOLI GTPase ObgE/CgtA (Gene Name=obgE)

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