Structure of PDB 5ndv Chain M1 Binding Site BS01

Receptor Information

>5ndv Chain M1 (length=169) Species: 559292 (Saccharomyces cerevisiae S288C)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

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): K16 V18 N20 S22 G24 S48 R51 Y52 V54 F57 I65 H68 R94 N95 S97 A98 T99 N101 G103 F104 G105 D107 G124 M125 D126 Y128 V130 R140 K142
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 G19 S43 R46 Y47 V49 F52 I60 H63 R89 N90 S92 A93 T94 N96 G98 F99 G100 D102 G119 M120 D121 Y123 V125 R135 K137

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• 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: Q3E757|RL11B_YEAST Large ribosomal subunit protein uL5B (Gene Name=RPL11B)