Structure of PDB 4rf9 Chain B Binding Site BS01

Receptor Information
>4rf9 Chain B (length=686) Species: 67755 (Anthopleura japonica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MADPETAAKFKSKNAFPDPLNDPKCNPKSLVKKYLTPKVFESLKNKKTKL
GITLWDCINSGVVNLDSGVGVYAGDEESYTLFGPLFDAIIEDYHSPYKLA
TGHNSDMNPAHVKAPDLDPANRYIRSTRIRVARSLKGYGLAPGVTKAHRL
EIEKKVVGVLTSLTGDLAGKYYPLSGMDEKTRQQLVDDHFLFKKGDRFLE
AAGINKEWPEGRGIYHNNDKTFLVWLNEEDHLRIISMEKGSDIGSVFSRL
CRAVNEIDKKLGFQHTKKHGYLTSCPSNLGTGMRASVHVKIPHAKEHPDF
ENILTKYHIQARGIEDAGVYDISNRRRLGLSEVQCVQDMYDGVKALMELE
KEAIAKKRSVFPEVLKNPEVKSLLRKYLTPELFDSLKDKKTAKGISLYDC
INSGVENLDSSCGVYAGDEECYTLFAPLFDKIVEDYHSPYKLANKHTSDM
NPEKVDAPNLDPEGTYIRSTRIRVARNVKGYALTPGLTRNERLDIERKVV
GVLSSLTGDLAGQYYPLTGMDEATRQKLVNDHFLFKKGDRFLEAAGVNKL
WPEGRGIFHNNDKTFLVWINEEDQLRIISMEKGSDIGSVFGRLCRAVNEI
DKQLGFQHTDAHGYLSGCPTNLGTGMRASVHVKIPKASAHPDFQKICDEF
HIQARDISNRRRLGLSEVQCVQDMYNGVKKLLEIEK
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain4rf9 Chain B Residue 801 [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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PDB4rf9 Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		S126 R128 R130 R233 R284 S286 H288
Binding residue
(residue number reindexed from 1)		S126 R128 R130 R233 R284 S286 H288
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R130 E229 R233 C275 S277 R284 R312
Catalytic site (residue number reindexed from 1) R130 E229 R233 C275 S277 R284 R312
Enzyme Commision number 2.7.3.3: arginine kinase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004054 arginine kinase activity
GO:0004111 creatine kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
Biological Process
GO:0016310 phosphorylation
GO:0046314 phosphocreatine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4rf9, PDBe:4rf9, PDBj:4rf9
PDBsum4rf9
PubMed25849389
UniProtO15992|KARG_ANTJA Arginine kinase

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