Structure of PDB 4jzt Chain A Binding Site BS01

Receptor Information
>4jzt Chain A (length=158) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYEFKDYYQNTVQLSFDDQPFSDSPKHVWVICRFGGKWLLTEHEDRGYEF
PGGKVEPMECAEEAALRAVKEETGARVKSLKYLGQYKVLGKEKVIVKNIY
FADIEKLEKQADYFETKGPVLFHELPENLSRNKKFSFIMKDSVLPISLKK
LKESGWIE
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=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)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain4jzt Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jzt Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D6 H27 K54 Y86 V88 K93 I95 K97 I138
Binding residue
(residue number reindexed from 1)		D6 H27 K54 Y86 V88 K93 I95 K97 I138
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) I31 K37
Catalytic site (residue number reindexed from 1) I31 K37
Enzyme Commision number 3.6.1.55: 8-oxo-dGTP diphosphatase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0046872 metal ion binding
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Cellular Component
External links
PDB RCSB:4jzt, PDBe:4jzt, PDBj:4jzt
PDBsum4jzt
PubMed23610407
UniProtO35013|YTKD_BACSU Putative 8-oxo-dGTP diphosphatase YtkD (Gene Name=ytkD)

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