Structure of PDB 5ded Chain B Binding Site BS02

Receptor Information
>5ded Chain B (length=191) Species: 1415167 (Bacillus subtilis PY79) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKQWERFLVPYRQAVEELKVKLKGIRTLYEYEDDHSPIEFVTGRVKPVAS
ILEKARRKSIPLHEIETMQDIAGLRIMCQFVDDIQIVKEMLFARKDFTVV
DQRDYIAEHKESGYRSYHLVVLYPLQTVSGEKHVLVEIQIRTLAMNFWAT
IEHSLNYKSGNEKVKLRLQRASEAASRLDEEMSEIRGEVAA
Ligand information
Ligand ID0O2
InChIInChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyKCPMACXZAITQAX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=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[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H18 N5 O20 P5
Nameguanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
ChEMBL
DrugBank
ZINCZINC000083923877
PDB chain5ded Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ded Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone.
Resolution2.942 Å
Binding residue
(original residue number in PDB)		R46 K48 K56 R59 K60 R105 Y107 K112 S114 Y116 H120 E139 Q141 A151 E154 H155
Binding residue
(residue number reindexed from 1)		R44 K46 K54 R57 K58 R103 Y105 K110 S112 Y114 H118 E137 Q139 A149 E152 H153
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.6.5: GTP diphosphokinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0008728 GTP diphosphokinase activity
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0015969 guanosine tetraphosphate metabolic process
GO:0015970 guanosine tetraphosphate biosynthetic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ded, PDBe:5ded, PDBj:5ded
PDBsum5ded
PubMed26460002
UniProtO31611|YJBM_BACSU GTP pyrophosphokinase YjbM (Gene Name=yjbM)

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