Structure of PDB 5ndw Chain L2 Binding Site BS02

Receptor Information

>5ndw Chain L2 (length=252) Species: 559292 (Saccharomyces cerevisiae S288C)

GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHD
SGRGAPLAKVVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNV
LPLGSVPEGTIVSNVEEKPGDRGALARASGNYVIIIGHNPDENKTRVRLP
SGAKKVISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPKTRG
VAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAARRTGLLRGSQK
TQ

Ligand information

>5ndw Chain 2 (length=1770)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuacuacaugguauaacugu
gguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagaga
uguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucau
aauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaau
uucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuca
acggguaacggggaauaaggguucgauuccggagagggagccugagaaac
ggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaa
uucagggagguagugacaauaaauaacgauacagggcccauucgggucuu
guaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagg
gcaagucuggugccagcagccgcgguaauuccagcuccaauagcguauau
uaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguugg
ccggucggauuuccaacggggccuuuccuucuggcuaaccuugaguccuu
guggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguuca
aagcaggcguauugcucgaauauauuagcauggaauaauagaauaggacg
uuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggga
cggucgggggcaucaguauucaauugucagaggugaaauucuuggauuua
uugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaauc
aagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuua
accauaaacuaugccgacuagggaucgggugguguuuuuuuaaugaccca
cucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaugg
ucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagug
gagccugcggcuuaauuugacucaacacggggaaacucaccagguccaga
cacaauaaggauugacagauugagagcucuuucuugauuuuguggguggu
ggugcauggccguucuuaguugguggagugauuugucugcuuaauugcga
uaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcuggu
uauccacuucuuagagggacuaucgguuucaagccgauggaaguuugagg
caauaacaggucugugaugcccuuagacguucugggccgcacgcgcgcua
cacugacggagccagcgagucuaaccuuggccgagaggucuugguaaucu
ugugaaacuccgucgugcuggggauagagcauuguaauuauugcucuuca
acgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacgucc
cugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuuagu
gaggccucaggaucugcuuagagaagccaucucagagcggagaauuugga
caaacuuggucauuuagaggaacuaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucau

...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<<..........>>...>>.>>......{{..
......[[[..{{..{{....[[[................<.....<<.<
<<.....>>>.>>......>.........<<<<<..<<....>>..>>>>
>[...((((((......<<<<<<<<<<<....>>>..............)
))))).....]...<<<<..<<<.....>>>.>>>>....]]]...}}}}
..]]].<<<....<<<....<<<<<<<<.......>>>>>>>>>>>....
..>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<.........
.>>>.>>.<.<<....>>.>...]]]]]].........<<<....<<<..
...>>>..>>>...............<<<<<.<<.<<........>>.>>
.>>.>>>......<<..<...........>..>>.........<<<<<((
......<<<<.....<<..))>>.......>>>>.>>>>>..))))))]]
]].........[[[{{.......{{...[[[.{{....<<<<<<.<<<<<
....<.>.....>>>>>.>>>>>>....<<<<<<...........<....
...>...........>>>>>>...<<<<<.<<.......<<...<.....
..>..<<<.....>>>....>>......>>.>>..>>>.........[[[
..((((((((....>>>>>>>>.)))))))).]]].....}}....<<<<
<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>......>.>
>>>>>..>>.......<<....>>...>>>>...>>>>>.>>>...]]].
..}}......<<<<<<<...<...<<<<.........>>>>...>>>>>>
>>..........<<<.<<.<<<..<<<<<<<<.<<<........>>>>>>
>>>>>..>>>...<<..}}>>...>>.....>>>.]]].<<<......<<
<<....>>>>....>>>..]]]]..<<<<<.<<<<<<<..<<.<<<<<<.
.<<<.<<<<<.......<<........>>..........<<<<<.<....
<<<<<........<<.<<<........>>>.>>......>>>>>.<.<<.
<<<..<<<<<<<<<....<<<.<<<<<....>>>...<<<......>>>.
..>>.>>>....<<<<..<<..<<<<..<<<<<.<<<<<<....>>>>>>
...>>>>>..>>>>.>>....<<<<<<.....>>>>>>........>>>>
....>>>.>>>...>.>>>>>>>>....>.>>>>>....>.>>>>.>>>.
....<<<<<<<......<<.....<<..<<<<....>>>>..>>....>>
.......>>>>>>>...........<<<<<<..........>>>>>>...
.......>>>>>>....<<<<<<<<.......>>>>>>>>......>>..
.>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<.<<<
..<.<<..<...<<<<<<<.<<.........>>.>>>>>>>...>..>>.
>..>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<
....>>>>>>>>>.......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): G248 S249 K251
• Binding residue (residue number reindexed from 1): G247 S248 K250

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P0CX45|RL2A_YEAST Large ribosomal subunit protein uL2A (Gene Name=RPL2A)