Structure of PDB 2i4m Chain B Binding Site BS01

Receptor Information
>2i4m Chain B (length=441) Species: 1076 (Rhodopseudomonas palustris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGH
RVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIA
DRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRF
GVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRA
ETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPII
KQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSM
KANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFR
VTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLI
GIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVARLT
Ligand information
Ligand IDP5A
InChIInChI=1S/C15H21N7O7S/c16-12-9-13(19-5-18-12)22(6-20-9)15-11(24)10(23)8(29-15)4-28-30(26,27)21-14(25)7-2-1-3-17-7/h5-8,10-11,15,17,23-24H,1-4H2,(H,21,25)(H2,16,18,19)/t7-,8+,10+,11+,15+/m0/s1
InChIKeyLKVJEMXWEODCAY-JVEUSOJLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[S](=O)(=O)NC(=O)[CH]4CCCN4)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)[C@@H]4CCCN4)[C@@H](O)[C@H]3O
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C4NCCC4
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@@H]4CCCN4)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C4CCCN4)O)O)N
FormulaC15 H21 N7 O7 S
Name'5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE
ChEMBLCHEMBL1163086
DrugBankDB02510
ZINCZINC000013542769
PDB chain2i4m Chain B Residue 439 [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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PDB2i4m Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a cis-Editing Domain.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		T109 E111 R140 F155 M157 D159 Y161 I202 E282 V283 G284 Q285 F287 Y316 G317 G319 R322
Binding residue
(residue number reindexed from 1)		T112 E114 R143 F158 M160 D162 Y164 I205 E285 V286 G287 Q288 F290 Y319 G320 G322 R325
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) E111 R140 M157 D159 Y161 I246 H312
Catalytic site (residue number reindexed from 1) E114 R143 M160 D162 Y164 I249 H315
Enzyme Commision number 6.1.1.15: proline--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004827 proline-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006433 prolyl-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:2i4m, PDBe:2i4m, PDBj:2i4m
PDBsum2i4m
PubMed17027500
UniProtQ6N5P6|SYP_RHOPA Proline--tRNA ligase (Gene Name=proS)

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