Structure of PDB 2zue Chain A Binding Site BS02

Receptor Information
>2zue Chain A (length=628) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LMEIRESVKERIEEIIKEIAPQWEGEIELKETPDPKLGDFGTPIAFKLAK
LLKRPPIEIAEKIVEKLKLNLPEGIKDVKAVNGYINVFIDYPHFARILIN
DILAKGDRFGSSEIGKGKKVIVEHTSVNPTKPLHMGHARNAILGDVMARI
LRFLGYEVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDN
PIDHALGLLYVEVNRRLEDNPELENEIRDIMKKLESGELYGRKLAEEVVR
AQMVTTYKLGVKYDLLVWESDIVRRKLFEIALELLSKNENFYIPSDGKYR
GAFVMDLRKLFPDMKNPILVLRRSDGTATYTGKDIAYHLWKFGKIDVDLL
YKEWDSTTWTTAPDGKSMPNKFGNANIVINVIGAEQKHPQLAIKYALQLL
GFEDAAANLYHLAYEHVERPEGKFSGRKGTWVGFTVDEVIQEAVKRAREL
IEEKNPALSDEEKAEVAEKVGIGAIRYNLIKYSPDKKIIFRWEDVLNFEG
ESAPYIQYAHARCSSILRKAEEEGIKVDPETLFKNADFTKLSERERELVI
MLSKFPRIVEQAGKDVKPHLIAWFANELASLFNKFYMDHPVLKAEEGVRE
ARLLLVMAVEQVLKNALYLMGIEAPERM
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 chain2zue Chain A Residue 700 [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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PDB2zue Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)
Resolution2.0 Å
Binding residue
(original residue number in PDB)		V128 N129 K132 H135 G137 H138 I383 G384 E386 Y415 H417 V418
Binding residue
(residue number reindexed from 1)		V127 N128 K131 H134 G136 H137 I382 G383 E385 Y414 H416 V417
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K132 H135 H138
Catalytic site (residue number reindexed from 1) K131 H134 H137
Enzyme Commision number 6.1.1.19: arginine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004814 arginine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006420 arginyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2zue, PDBe:2zue, PDBj:2zue
PDBsum2zue
PubMed19656186
UniProtO59147|SYR_PYRHO Arginine--tRNA ligase (Gene Name=argS)

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