Structure of PDB 5ndw Chain C4 Binding Site BS01

Receptor Information

>5ndw Chain C4 (length=127) Species: 559292 (Saccharomyces cerevisiae S288C)

SQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGL
RIGRIEDVTPVPSDSTRKKGGRRGRRL

Ligand information

>5ndw Chain 2 (length=1770)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuacuacaugguauaacugu
gguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagaga
uguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucau
aauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaau
uucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuca
acggguaacggggaauaaggguucgauuccggagagggagccugagaaac
ggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaa
uucagggagguagugacaauaaauaacgauacagggcccauucgggucuu
guaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagg
gcaagucuggugccagcagccgcgguaauuccagcuccaauagcguauau
uaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguugg
ccggucggauuuccaacggggccuuuccuucuggcuaaccuugaguccuu
guggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguuca
aagcaggcguauugcucgaauauauuagcauggaauaauagaauaggacg
uuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggga
cggucgggggcaucaguauucaauugucagaggugaaauucuuggauuua
uugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaauc
aagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuua
accauaaacuaugccgacuagggaucgggugguguuuuuuuaaugaccca
cucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaugg
ucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagug
gagccugcggcuuaauuugacucaacacggggaaacucaccagguccaga
cacaauaaggauugacagauugagagcucuuucuugauuuuguggguggu
ggugcauggccguucuuaguugguggagugauuugucugcuuaauugcga
uaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcuggu
uauccacuucuuagagggacuaucgguuucaagccgauggaaguuugagg
caauaacaggucugugaugcccuuagacguucugggccgcacgcgcgcua
cacugacggagccagcgagucuaaccuuggccgagaggucuugguaaucu
ugugaaacuccgucgugcuggggauagagcauuguaauuauugcucuuca
acgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacgucc
cugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuuagu
gaggccucaggaucugcuuagagaagccaucucagagcggagaauuugga
caaacuuggucauuuagaggaacuaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucau

...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<<..........>>...>>.>>......{{..
......[[[..{{..{{....[[[................<.....<<.<
<<.....>>>.>>......>.........<<<<<..<<....>>..>>>>
>[...((((((......<<<<<<<<<<<....>>>..............)
))))).....]...<<<<..<<<.....>>>.>>>>....]]]...}}}}
..]]].<<<....<<<....<<<<<<<<.......>>>>>>>>>>>....
..>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<.........
.>>>.>>.<.<<....>>.>...]]]]]].........<<<....<<<..
...>>>..>>>...............<<<<<.<<.<<........>>.>>
.>>.>>>......<<..<...........>..>>.........<<<<<((
......<<<<.....<<..))>>.......>>>>.>>>>>..))))))]]
]].........[[[{{.......{{...[[[.{{....<<<<<<.<<<<<
....<.>.....>>>>>.>>>>>>....<<<<<<...........<....
...>...........>>>>>>...<<<<<.<<.......<<...<.....
..>..<<<.....>>>....>>......>>.>>..>>>.........[[[
..((((((((....>>>>>>>>.)))))))).]]].....}}....<<<<
<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>......>.>
>>>>>..>>.......<<....>>...>>>>...>>>>>.>>>...]]].
..}}......<<<<<<<...<...<<<<.........>>>>...>>>>>>
>>..........<<<.<<.<<<..<<<<<<<<.<<<........>>>>>>
>>>>>..>>>...<<..}}>>...>>.....>>>.]]].<<<......<<
<<....>>>>....>>>..]]]]..<<<<<.<<<<<<<..<<.<<<<<<.
.<<<.<<<<<.......<<........>>..........<<<<<.<....
<<<<<........<<.<<<........>>>.>>......>>>>>.<.<<.
<<<..<<<<<<<<<....<<<.<<<<<....>>>...<<<......>>>.
..>>.>>>....<<<<..<<..<<<<..<<<<<.<<<<<<....>>>>>>
...>>>>>..>>>>.>>....<<<<<<.....>>>>>>........>>>>
....>>>.>>>...>.>>>>>>>>....>.>>>>>....>.>>>>.>>>.
....<<<<<<<......<<.....<<..<<<<....>>>>..>>....>>
.......>>>>>>>...........<<<<<<..........>>>>>>...
.......>>>>>>....<<<<<<<<.......>>>>>>>>......>>..
.>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<.<<<
..<.<<..<...<<<<<<<.<<.........>>.>>>>>>>...>..>>.
>..>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<
....>>>>>>>>>.......

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): R18 N24 D25 F27 H29 G35 K36 E37 T38 R41 T43 G45 M46 D51 R52 E54 R90 V121 P122 S123 D124 S125 T126 R127 K129 G130 R132 R133 R135 R136
• Binding residue (residue number reindexed from 1): R8 N14 D15 F17 H19 G25 K26 E27 T28 R31 T33 G35 M36 D41 R42 E44 R80 V111 P112 S113 D114 S115 T116 R117 K119 G120 R122 R123 R125 R126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P39516|RS14B_YEAST Small ribosomal subunit protein uS11B (Gene Name=RPS14B)