Structure of PDB 5ndg Chain L5 Binding Site BS01

Receptor Information

>5ndg Chain L5 (length=294) Species: 4932 (Saccharomyces cerevisiae)

AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRL
VVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYAT
GLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQ
RTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFG
GHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADP
AFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAG

Ligand information

>5ndg Chain 1 (length=3078)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccgcggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguuugaugcc
cugacgaguaggcaggcguggaggucagugacgaagccuagaccguaagg
ucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauuc
aaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagca
guuggacguggguuagucgauccuaagagauggggaagcuccguuucaaa
ggccugaugcaggccaccaucgaaagggaauccgguuaagauuccggaac
cuggauauggauucuucacgguaacguaacugaauguggagacgucggcg
cgagcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccgga
auugguuuauccggagauggggucuuauggcuggaagaggccagcaccuu
ugcuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaa
uaguuuucaugccaggucguacugauaaccgcagcaggucuccaagguga
acagccucuaguugauagaauaauguagauaagggaagucggcaaaauag
auccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuu
agaacugguacggacaaggggaaucugacugucuaauuaaaacauagcau
ugcgauggucagaaagugauguugacgcaaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggauuaacgagauucccacugucccuaucuacuaucuag
cgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaag
acccuguugagcuugacucuaguuugacauugugaagaguuucuuuacuu
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: 5ndg Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): K5 K8 Y12 R15 F16 Q17 P19 R23 G26 T28 Y31 R35 L36 K43 K48 P139 R140 P141 F142 F145 L146 I148 R152 T153 P174 H175 S176 R179
• Binding residue (residue number reindexed from 1): K4 K7 Y11 R14 F15 Q16 P18 R22 G25 T27 Y30 R34 L35 K42 K47 P138 R139 P140 F141 F144 L145 I147 R151 T152 P173 H174 S175 R178

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• 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:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)