Structure of PDB 5mbs Chain A Binding Site BS01

Receptor Information
>5mbs Chain A (length=403) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPVVAIVGRPNVGKSTIFNRIAERISIVEDTPDRIYSSAEWLNYDFNLID
TGQIRQQAEIAMDEADVIIFMVNGREGVTAADEEVAKILYRTKKPVVLAV
NKLDNMRANIYDFYSLGFGEPYPISGTHGLGLGDLLDAVAEHFKNIPETK
YNEEVIQFCLIGRPNVGKSSLVNAMLGEERVIVAVDTSFTYNQQEFVIVD
TAGMRKKGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGIIEQDKRIA
GYAHEAGKAVVIVVNKWDAVDSTMKEFEENIRDHFQFLDYAPILFMSALT
KKRIHTLMPAIIKASENHSLRVQTNVLNDVIMDAVAMNPTPTHNGSRLKI
YYATQVSVKPPSFVVFVNDPELMHFSYERFLENRIRDAFGFEGTPIKIFA
RAR
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 chain5mbs 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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PDB5mbs Crystal structure of Bacillus subtilis EngA in space group P21
Resolution3.2 Å
Binding residue
(original residue number in PDB)		P184 N185 V186 G187 K188 S189 S190 K236 K295
Binding residue
(residue number reindexed from 1)		P164 N165 V166 G167 K168 S169 S170 K207 K266
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005525 GTP binding
GO:0043022 ribosome binding
Biological Process
GO:0042254 ribosome biogenesis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5mbs, PDBe:5mbs, PDBj:5mbs
PDBsum5mbs
PubMed
UniProtP50743|DER_BACSU GTPase Der (Gene Name=der)

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