Structure of PDB 5ybi Chain A Binding Site BS01

Receptor Information
>5ybi Chain A (length=337) Species: 623 (Shigella flexneri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMHTQVGRGLLGAVVNPLGEVTDKFAVTDNSEILYRPVDNAPPLYSERA
AIEKPFLTGIKVIDSLLTCGEGQRMGIFASAGCGKTFLMNMLIEHSGADI
YVIGLIGERGREVTETVDYLKNSEKKSRCVLVYATSDYSSVDRCNAAYIA
TAIAEFFRTEGHKVALFIDSLTRYARALRDVALAAGESPARRGYPVSVFD
SLPRLLERPGKLKAGGSITAFYTVLLEDDDFDPLAEEVRSILDGHIYLSR
NLAQKGQFPAIDSLKSISRVFTQVVDEKHRIMAAAFRELLSEIEELRTIS
QDKIYNKISVVESFLKQDYRLGFTYEQTMELIGETIR
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[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
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5ybi Chain A Residue 505 [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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PDB5ybi Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri.
Resolution2.268 Å
Binding residue
(original residue number in PDB)		G162 G164 K165 T166 F167 F339 Y412
Binding residue
(residue number reindexed from 1)		G82 G84 K85 T86 F87 F258 Y319
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.49,Kd=322.48uM
Enzymatic activity
Catalytic site (original residue number in PDB) K165 E188 R189 R350
Catalytic site (residue number reindexed from 1) K85 E108 R109 R269
Enzyme Commision number 7.4.2.8: protein-secreting ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0009058 biosynthetic process
GO:0030254 protein secretion by the type III secretion system
Cellular Component
GO:0005737 cytoplasm
GO:0030257 type III protein secretion system complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ybi, PDBe:5ybi, PDBj:5ybi
PDBsum5ybi
PubMed30013545
UniProtP0A1C1|SCTN_SHIFL Type 3 secretion system ATPase (Gene Name=sctN)

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