Structure of PDB 5ndv Chain L7 Binding Site BS01

Receptor Information

>5ndv Chain L7 (length=226) Species: 559292 (Saccharomyces cerevisiae S288C)

QQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRD
AKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVK
VTKATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAI
IEANLGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPR
KFKHFIQGGSFGNREEFINKLVKSMN

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): R33 K34 N37 R41 R60 R67 K70 K90 G91 I92 N93 K94 P97 K98 K101 L105 R107 R110 I111 N112 K121 A122 E125 L126 S142 R145 K150 R151 K158 Q159 R160 D165 K196 N200 K206 L207 S208 N209 P210 S211 W214 R218 K219
• Binding residue (residue number reindexed from 1): R15 K16 N19 R23 R42 R49 K52 K72 G73 I74 N75 K76 P79 K80 K83 L87 R89 R92 I93 N94 K103 A104 E107 L108 S124 R127 K132 R133 K140 Q141 R142 D147 K178 N182 K188 L189 S190 N191 P192 S193 W196 R200 K201

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

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: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)