Structure of PDB 5ndv Chain O6 Binding Site BS01

Receptor Information

>5ndv Chain O6 (length=97) Species: 559292 (Saccharomyces cerevisiae S288C)

TVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLS
PYERRLIDLIRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASR

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): G14 K15 K25 I26 S27 Y28 K30 G31 A32 A33 S34 N35 R36 T37 R41 Y53 D59 N63 R68 K75 R76 L77 G78 F80 R82 K84 K86
• Binding residue (residue number reindexed from 1): G13 K14 K24 I25 S26 Y27 K29 G30 A31 A32 S33 N34 R35 T36 R40 Y52 D58 N62 R67 K74 R75 L76 G77 F79 R81 K83 K85

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

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: P05745|RL36A_YEAST Large ribosomal subunit protein eL36A (Gene Name=RPL36A)