Structure of PDB 4edk Chain A Binding Site BS01

Receptor Information
>4edk Chain A (length=321) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNADDLQMIEMHELIQEFYYYALTKTVEGEQALTYLQERGFTDALIKERG
IGFAPDSSHFCHDFLQKKGYDIELAYEAGLLSRNEENFSYYDRFRNRIMF
PLKNAQGRIVGYSGRTYTGQEPKYLNSPETPIFQKRKLLYNLDKARKSIR
KLDEIVLLEGFMDVIKSDTAGLKNVVATMGTQLSDEHITFIRKLTSNITL
MFDGDFAGSEATLKTGQHLLQQGLNVFVIQLPSGMDPDEYIGKYGNDAFT
TFVKNDKKSFAHYKVSILKDEIAHNDLSYERYLKELSHDISLMKSSILQQ
KAINDVAPFFNVSPEQLANEI
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 chain4edk Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4edk Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		R146 R222 K230 Y231 G287
Binding residue
(residue number reindexed from 1)		R39 R115 K123 Y124 G180
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.101: DNA primase DnaG.
Gene Ontology
Molecular Function
GO:0003896 DNA primase activity
Biological Process
GO:0006269 DNA replication, synthesis of primer

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Molecular Function
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Biological Process
External links
PDB RCSB:4edk, PDBe:4edk, PDBj:4edk
PDBsum4edk
PubMed22795082
UniProtO05338|DNAG_STAAU DNA primase (Gene Name=dnaG)

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