Structure of PDB 5ndg Chain L7 Binding Site BS01

Receptor Information

>5ndg Chain L7 (length=222) Species: 4932 (Saccharomyces cerevisiae)

AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAA
GSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKA
TLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEAN
LGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKH
FIQGGSFGNREEFINKLVKSMN

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): R30 K34 N37 R41 R60 R67 K70 K90 G91 I92 N93 K94 P97 K98 K101 L105 R107 R110 I111 N112 K121 A122 E125 L126 Y141 S142 R145 K150 K155 K158 Q159 R160 D165 K196 K206 S208 N209 P210 S211 G213 W214 P217 R218 K219 K241
• Binding residue (residue number reindexed from 1): R8 K12 N15 R19 R38 R45 K48 K68 G69 I70 N71 K72 P75 K76 K79 L83 R85 R88 I89 N90 K99 A100 E103 L104 Y119 S120 R123 K128 K133 K136 Q137 R138 D143 K174 K184 S186 N187 P188 S189 G191 W192 P195 R196 K197 K219

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:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)