Structure of PDB 5ndv Chain O0 Binding Site BS01

Receptor Information

>5ndv Chain O0 (length=97) Species: 559292 (Saccharomyces cerevisiae S288C)

SINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEY
YAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

Ligand information

>5ndv Chain 1 (length=3078)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagaggccagcaucaguu
uugguggcaggauaaauccauaggaauguagcuugccucgguaaguauua
uagccugugggaauacugccagcugggacugaggacugcgacguaaguca
aggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaa
ggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaau
gaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgauc
cugaugucuucggauggauuugaguaagagcauagcuguugggacccgaa
agauggugaacuaugccugaauagggugaagccagaggaaacucuggugg
aggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauag
gggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuuc
ccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugau
uagagguuccgggguccuugaccuauucucaaacuuuaaauauguaagaa
guccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagug
ggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguaga
guuaaggugccggaauacacgcucaucagacaccacaaaagguguuaguu
caucuagacagccggccggccgaaugaacuagcccugaaaauggauggcg
cucaagcguguuaccuauacucuaccgucaggguuugaugcccugacgag
uaggcaggcguggaggucagugacgaagccuagaccguaaggucgggucg
aacggccucuagugcagaucuuggugguaguagcaaauauucaaaugaga
acuuugaagacugaaguggggaaagguuccacgucaacagcaguuggacg
uggguuagucgauccuaagagauggggaagcuccguuucaaaggccugau
uuuaugcaggccaccaucgaaagggaauccgguuaagauuccggaaccug
gauauggauucuucacgguaacguaacugaauguggagacgucggcgcga
gcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauu
gguuuauccggagauggggucuuauggcuggaagaggccagcaccuugcu
ggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaauagu
uuucaugccaggucguacugauaaccgcagcaggucuccaaggugaacag
ccucuaguugauagaauaauguagauaagggaagucggcaaaauagaucc
guaacuucgggauaaggauuggcucuaagggucggaacgaucaacuuaga
acugguacggacaaggggaaucugacugucuaauuaaaacauagcauugc
gauggucagaaagugauguugacgcaaugugauuucugcccagugcucug
aaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggaguaa
cuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacgc
gcaugaauggauuaacgagauucccacugucccuaucuacuaucuagcga
aaccacagccaagggaacgggcuuggcagaaucagcggggaaagaagacc
cuguugagcuugacucuaguuugacauugugaagagacguuucuuuacuu
auucaaugaagcggagcuggaauucauuuuccacguucuagcauucaagg
ucccauucggggcugauccggguugaagacauugucagguggggaguuug
gcuggggcggcacaucuguuaaacgauaacgcagauguccuaaggggggc
ucauggagaacagaaaucuccaguagaacaaaaggguaaaagcccccuug
auuuugauuuucagugugaauacaaaccaugaaaguguggccuaucgauc
cuuuagucccucggaauuugaggcuagaggugccagaaaaguuaccacag
ggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuuuga
uucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaagcg
uuggauuguucacccacuaauagggaacgugagcuggguuuagaccgucg
ugagacagguuaguuuuacccuacugaugaauguuaccgcaauaguaauu
gaacuuaguacgagaggaacaguucauucggauaauugguuuuugcggcu
gucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcugaa
cgccucuaagucagaauccaugcuagaacgcggugauuugcuccacacaa
uauagauggauacgaauaaggcguccuuguggcgucgcugaaccauagca
ggcuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaa
uugcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaug
uacaacgggguauuguaagcaguagaguagccuuguuguuacgaucugcu
gagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<<.<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>>..>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<
<..((((((>>>>>..>>>...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<....<<<<<<<.<<<<<
<<<<<<<<<<.....<<<<<<<<<....<.<<<<<......>>>>>>...
...>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>>.
....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<<<
<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...<<
....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<<<
<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<..
<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>..
...>>>...<<<<.<<.<<........>>>>>>>>....>>>>>>>>>..
.<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.<<
<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<<.
...<<<<<..<<<...>>>>>>>>....>>>..>.>>.....>>>>>...
<<<<.<<<<.........>>>>.>>>>.....>>>>>.>>>>>>>>.>>.
.<<<<.<<<<<.....>>>>>.>>>>....<<<..[...>>>...<<<<<
<<..<<<<(((.....<<<<<<......<.....]....<<<.<<<<<<<
<<<.......<<<<..>>>>...>>>>>>>>>>>>>..........))).
>....>>>>>>.>>>>..>>>>>>><<<<<<<<<.....>>>>>>>>>..
..>>>>>><.<<<<<<<..<<......<<<<.<<<<....>>>>>>>>..
.>>.>>>>>>>..>.....>>>>>><<.....<<.....<<<<<<.....
..>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>
>>>....((<<<<<<...<<....<<<....>>>........<<<<<<..
......>>>>>>....>>....>>...<<<<<........>>>>>))<<<
<.<<<<<<<.....<<<....>>>.......<<<<<<...<<<<.<<<<<
<<.<<<<<<<<<<..[[[..>>>>>><...<<<<<<...<<<<<<....<
<<.....>>>....>>>>>>...>.>>>>>....><<<<<<<.....>>>
>>>>>>>>...>>>>>>>.>>>>.........>>>>>>..........>>
>..>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.....>
>>>..>>>>..<<<<.....<<<<<<<.<<...............<<<<<
...............>>>>><<.<<<<<<<<<<<...>>>>>..>>>>>>
.>>............<<<<<<<<<..<<<.........>>>..<<<<<<<
....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<..
..<<<.....<<<<....>>>>.....>>>.>>>>..>>>>><<<<<<..
.....>>>>>>........<...........<<<<<.......>>>>>..
...>.....>>....>>.>>>>>>>.....>>.>>>>>>>..>>>>>>..
..>>....<<<<<........>>>>>....<<<<<..<<<.<<......<
<<<.<<<<<<..<<<<..<<<<<<<<..<<<<<<<<<..>>>>>>>>>..
.<<<<<.....<<<<..<<<..........>>>...............<<
<<<<....>>>>>>..>>>>..>>>>>.....>>>>>>>>...>>>>...
<<<.....>>>..<<<<<<...........>>>>>>..<<...<<<<<<<
...<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>..
.<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>)))......<
<<<<<<..<<<<.))))))>>>>>>>>>>>.........>>>>..>>>>>
>.......<<.<...<<<<<<...<<.......>>...>>>>>>....>.
>.>.......<<<<<.<<<<<<..<.<<<<<<<......>>>>>>>...>
.<<<.........>>>.....>>>>>..>...>>>.>>....<<<<<<<.
...>>>.>>>>....>>..>>>.>>>>>....<<<<<<<<..<<<<.<.<
<<<<<...............>>>>>>.><<<<<...<<<<....<<<<<<
<<<.]]]..>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<...
........>>>>>...>>>>.>>>>....>>>>>>>>...<<<<<<.<<<
.<<....<<..........<<<<<<.....>>>>>>......>>......
.<<<<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>>>>...
..........>>.>>>.>>>>>>..<<<<<....................
.<<<<<<<<<.<<<....<<<<....<<<<<......>>>>>...>>>>.
..>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): L25 G26 Y27 K28 S29 P49 V50 R52 K53 S54 E57 L84 F85 R86 V87 G88
• Binding residue (residue number reindexed from 1): L17 G18 Y19 K20 S21 P41 V42 R44 K45 S46 E49 L76 F77 R78 V79 G80

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0030627 pre-mRNA 5'-splice site binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0048025 negative regulation of mRNA splicing, via spliceosome

Cellular Component

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

External links

• PDB: RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
• PDBsum: 5ndv
• PubMed: 29208708
• UniProt: P14120|RL30_YEAST Large ribosomal subunit protein eL30 (Gene Name=RPL30)