Structure of PDB 4dct Chain A Binding Site BS02

Receptor Information
>4dct Chain A (length=401) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPVVAIVGRPNVGKSTIFNIAGERISRIYSSAEWLNYDFNLIDTGGPFLA
QIRQQAEIAMDEADVIIFMVNGREGVTAADEEVAKILYRTKKPVVLAVNK
LNIYDFYSLGFGEPYPISGTHGLGLGDLLDAVAEHFKNIPETKYNEEVIQ
FCLIGRPNVGKSSLVNAMLGEERVIVSNDAVDTSFTYNQQEFVIVDTAGM
RKKGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGIIEQDKRIAGYAH
EAGKAVVIVVNKWDAVDKDESTMKEFEENIRDHFQFLDYAPILFMSALTK
KRIHTLMPAIIKASENHSLRVQTNVLNDVIMDAVAMNPTPTHNGSRLKIY
YATQVSVKPPSFVVFVNDPELMHFSYERFLENRIRDAFGFEGTPIKIFAR
A
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 chain4dct Chain A Residue 502 [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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PDB4dct Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N13 G15 K16 S17 R93 N119 K120 S145
Binding residue
(residue number reindexed from 1)		N11 G13 K14 S15 R73 N99 K100 S118
Annotation score4
Binding affinityMOAD: Kd=8uM
Enzymatic activity
Catalytic site (original residue number in PDB) F20 E26
Catalytic site (residue number reindexed from 1) F18 E23
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005525 GTP binding
GO:0043022 ribosome binding
Biological Process
GO:0042254 ribosome biogenesis

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Molecular Function
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Biological Process
External links
PDB RCSB:4dct, PDBe:4dct, PDBj:4dct
PDBsum4dct
PubMed23056455
UniProtP50743|DER_BACSU GTPase Der (Gene Name=der)

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