Structure of PDB 5of3 Chain D Binding Site BS01

Receptor Information
>5of3 Chain D (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 D Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		Y48 F74 D101 D103 S173 N175 R176 H179 R244 L245 R247
Binding residue
(residue number reindexed from 1)		Y38 F64 D91 D93 S163 N165 R166 H169 R234 L235 R237
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

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

[Back to BioLiP]