Structure of PDB 4upa Chain A Binding Site BS01

Receptor Information
>4upa Chain A (length=515) Species: 5759 (Entamoeba histolytica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHMLSKQLFLNRCKDVEEYQKAGHNPWPHKFNVSITVPEFIAKYSGLEK
SQVSDDIVSVAGRVLSKRSSSSALMFIDLHDSQTKLQIMLNKSAYENKED
FVSLTKMIYRGDICGFTGHPTRTKTGELSLIPISGMILSPCLHMLPSMHY
GLGDQETRFRKRYLDLIVNPESVKNFVLRTKVVKAVRKYLDDKGFLEVET
PILNTIPGGATARPFITHHNQLDIQMYMRIAPELYLKELVVGGINRVYEI
GRLFRNEGIDQTHNPEFTTCEFYMAYADYNDIMKMTEELLGNMVKDITGG
STKLEIKKKMVLDFTAPFKRISYVHALEEKFGEKIPRPLDGPEALTFLKK
QAIRFNAICAEPQTTARVMDKLFGDLIEVDLVQPTFVCDQPQLMSPLAKY
HRSEPELTERFELFILKREIANAYTELNNPIVQRSNFEQQAKDKALVDEV
FLDAIEHAFPPTGGWGLGIDRLAMLLADVDNIKEVILFPTMRPEDELEKK
AREAKEDAMVAQEKA
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 chain4upa Chain A Residue 1584 [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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PDB4upa Crystal Structures of Entamoeba Histolytica Lysyl-tRNA Synthetase Reveal Conformational Changes Upon Lysine Binding and a Specific Helix Bundle Domain.
Resolution2.901 Å
Binding residue
(original residue number in PDB)		R251 H259 N260 F263 R539
Binding residue
(residue number reindexed from 1)		R255 H263 N264 F267 R471
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) R251 E253 T258 H259 E480 N483 R539
Catalytic site (residue number reindexed from 1) R255 E257 T262 H263 E419 N422 R471
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4upa, PDBe:4upa, PDBj:4upa
PDBsum4upa
PubMed25448989
UniProtC4M7X2

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