Structure of PDB 4edr Chain A Binding Site BS01

Receptor Information
>4edr 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 IDUTP
InChIInChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPGAVKCOVUIYSFO-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N2 O15 P3
NameURIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL336296
DrugBankDB04005
ZINCZINC000003861755
PDB chain4edr 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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PDB4edr Binding Mechanism of Metal-NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		R146 R222 K230 Y231 F268 G287
Binding residue
(residue number reindexed from 1)		R39 R115 K123 Y124 F161 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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4edr, PDBe:4edr, PDBj:4edr
PDBsum4edr
PubMed22795082
UniProtO05338|DNAG_STAAU DNA primase (Gene Name=dnaG)

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