Structure of PDB 5ee9 Chain A Binding Site BS01

Receptor Information
>5ee9 Chain A (length=357) Species: 39947 (Oryza sativa Japonica Group) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERPILGRFSSHLKIGIVGLPNVGKSTFFNIVTKLSIPAENFPFCTIDPNE
ARVYVPDERFDWLCQLYKPKSEVSAYLEINDIAGLVRNAFLSHIRAVDGI
FHVLRAFEDSVDPVRDLETIGEELRLKDIEFVQNKIDDLEKSMKRSNDKQ
LKLEHELCEKVKAHLEDGKDVRFGDWKSADIEILNTFQLLTAKPVVYLVN
MSEKDYQRKKNKFLPKIHAWVQEHGGETIIPFSCAFERLLADMPPDEAAK
YCAENQIASVIPKIIKTGFAAIHLIYFFTAGPDEVKCWQIRRQTKAPQAA
GTIHTDFERGFICAEVMKFDDLKELGSESAVKAAGKYRQEGKTYVVQDGD
IIFFKFN
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain5ee9 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ee9 ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses
Resolution2.75 Å
Binding residue
(original residue number in PDB)		N34 G36 K37 S38 T39 G97 F129 N230
Binding residue
(residue number reindexed from 1)		N21 G23 K24 S25 T26 G84 F107 N200
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0043023 ribosomal large subunit binding
GO:0046872 metal ion binding
Biological Process
GO:0009651 response to salt stress
GO:1900425 negative regulation of defense response to bacterium
GO:1901001 negative regulation of response to salt stress
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ee9, PDBe:5ee9, PDBj:5ee9
PDBsum5ee9
PubMed26912459
UniProtQ6Z1J6|OLA1_ORYSJ Obg-like ATPase 1 (Gene Name=YCHF1)

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