Structure of PDB 5of3 Chain A Binding Site BS04

Receptor Information
>5of3 Chain A (length=319) Species: 273057 (Saccharolobus solfataricus P2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNLIKSFFRNYYLNAELELPKDMELREFALQPFGSDTYVRHLSFSSSEEL
RDYLVNRNLPLHLFYSSARYQLPSARNMEEKAWMGSDLLFDIDADHLCKL
RSIRFCPVCGNAVVSEKCERDNVETLEYVEMTSECIKRGLEQTRNLVEIL
EDDFGLKPKVYFSGNRGFHVQVDCYGNCALLDSDERKEIAEYVMGIGVPG
YPGGSENAPGWVGRKNRGINGVTIDEQVTIDVKRLIRIPNSLHGKSGLIV
KRVPNLDDFEFNETLSPFTGYTIFLPYITIETEVLGSIIKLNRGIPIKIK
SSIGIYLHLRNLGEVKAYV
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain5of3 Chain C Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5of3 Primer synthesis by a eukaryotic-like archaeal primase is independent of its Fe-S cluster.
Resolution2.906 Å
Binding residue
(original residue number in PDB)		E89 E90
Binding residue
(residue number reindexed from 1)		E79 E80
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.-
Gene Ontology
Molecular Function
GO:0003896 DNA primase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006269 DNA replication, synthesis of primer
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:1990077 primosome complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5of3, PDBe:5of3, PDBj:5of3
PDBsum5of3
PubMed29167441
UniProtQ97Z83|PRIS_SACS2 DNA primase small subunit PriS (Gene Name=priS)

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