Structure of PDB 5ded Chain D Binding Site BS02

Receptor Information
>5ded Chain D (length=188) 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
IEHSLYKPEKVKLRLQRASEAASRLDEEMSEIRGVQEA
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 D Residue 302 [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)		K21 K25 E41 F42
Binding residue
(residue number reindexed from 1)		K19 K23 E39 F40
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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