Structure of PDB 5ndg Chain N1 Binding Site BS01

Receptor Information

>5ndg Chain N1 (length=159) Species: 4932 (Saccharomyces cerevisiae)

GKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKG
MPHKFYQGKTGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKC
RQEFLERVKANAAKRAEAKAQGVAVQLKRQPAQPRESRIVSTEGNVPQTL
APVPYETFI

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): G2 K3 S4 H5 G6 Y7 R8 S9 R10 R12 Y13 M14 Q16 R17 F19 H22 G23 K35 D41 K43 S47 Q49 K50 G51 H54 K55 Y57 Q58 G59 K60 T61 T68 K69 S70 S71 K78 R83 L85 K87 R88 L89 N90 K100 C101 R102 E104 F105 R108 N112 K120 L128 K129 R130
• Binding residue (residue number reindexed from 1): G1 K2 S3 H4 G5 Y6 R7 S8 R9 R11 Y12 M13 Q15 R16 F18 H21 G22 K34 D40 K42 S46 Q48 K49 G50 H53 K54 Y56 Q57 G58 K59 T60 T67 K68 S69 S70 K77 R82 L84 K86 R87 L88 N89 K99 C100 R101 E103 F104 R107 N111 K119 L127 K128 R129

Gene Ontology

Molecular Function

• 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:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: Q02753|RL21A_YEAST Large ribosomal subunit protein eL21A (Gene Name=RPL21A)