Structure of PDB 4dcs Chain A Binding Site BS01

Receptor Information
>4dcs Chain A (length=406) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPVVAIVGRPNVGKSTIFNRIAGERISRIYSSAEWLNYDFNLIDTGGPFL
AQIRQQAEIAMDEADVIIFMVNGREGVTAADEEVAKILYRTKKPVVLAVN
KLMRANIYDFYSLGFGEPYPISGTHGLGLGDLLDAVAEHFKNIPETKYNE
EVIQFCLIGRPNVGKSSLVNAMLGEERVIVSNDAVDTSFTYNQQEFVIVD
TAGMRKKGKVYETTEKYSVLRALKAIDRSEVVAVVLDGEEGIIEQDKRIA
GYAHEAGKAVVIVVNKWDAVDKDESTMKEFEENIRDHFQFLDYAPILFMS
ALTKKRIHTLMPAIIKASENHSLRVQTNVLNDVIMDAVAMNPTPTHNGSR
LKIYYATQVSVKPPSFVVFVNDPELMHFSYERFLENRIRDAFGFEGTPIK
IFARAR
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 chain4dcs 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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PDB4dcs Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		N185 V186 G187 K188 S189 S190 K236 N294 K295 D297 S329 L331
Binding residue
(residue number reindexed from 1)		N162 V163 G164 K165 S166 S167 K207 N265 K266 D268 S300 L302
Annotation score4
Binding affinityMOAD: Kd=8uM
PDBbind-CN: -logKd/Ki=5.10,Kd=8.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) F20 E26
Catalytic site (residue number reindexed from 1) F18 E24
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:4dcs, PDBe:4dcs, PDBj:4dcs
PDBsum4dcs
PubMed23056455
UniProtP50743|DER_BACSU GTPase Der (Gene Name=der)

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