Structure of PDB 5ndg Chain D9 Binding Site BS01

Receptor Information

>5ndg Chain D9 (length=53) Species: 4932 (Saccharomyces cerevisiae)

ENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFN
KFR

Ligand information

>5ndg Chain 2 (length=1688)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuacaugguauaacuguggu
aauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagaugu
auuuauuagauaaaaaaucaagaugauucauaauaacuuuucgaaucgca
uggccuugugcuggcgaugguucauucaaauuucugcccuaucaacuuuc
gaugguaggauaguggccuaccaugguuucaacggguaacggggaauaag
gguucgauuccggagagggagccugagaaacggcuaccacauccaaggaa
ggcagcaggcgcgcaaauuacccaauccuaauucagggagguagugacaa
uaaauaacgauacagggccuuguaauuggaaugaguacaauguaaauacc
uuaacgaggaacaauuggagggcaagucuggugccagcagccgcgguaau
uccagcuccaauagcguauauuaaaguuguugcaguuaaaaagcucguag
uugaacuuugggcccgguugguuuccaacggggccuuuccuucggacuuu
uacuuugaaaaaauuagaguguucaaagcaggcguauugcucgaauauau
uagcauggaauaauagaauaggacguuugguucuauuuuguugguuucua
ggaccaucguaaugauuaauagggacggucgggggcaucaguauucaauu
gucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaagca
uuugccaaggacguuuucauuaaucaagaacgaaaguuaggggaucgaag
augaucagauaccgucguagucuuaaccauaaacuaugccgacuagggau
cgggugguguuuuuuuaaugacccacucggcaccuuacgagaaaucaaag
ucuuuggguucuggggggaguauggucgcaaggcugaaacuuaaaggaau
ugacggaagggcaccaccaggaguggagccugcggcuuaauuugacucaa
cacggggaaacucaccagguccagacacaauaaggauugacagauugaga
gcucuuucuugauuuugugggugguggugcauggccguucuuaguuggug
gagugauuugucugcuuaauugcgauaacgaacgagaccuuaaccuacua
aauaguggugcuagcauuugcugguuauccacuucuuagagggacuaucg
guuucaagccgauggaaguuugaggcaauaacaggucugugaugcccuua
gacguucugggccgcacgcgcgcuacacugacggagccagcgagucuaac
cuuggccgagaggucuugguaaucuugugaaacuccgucgugcuggggau
agagcauuguaauuauugcucuucaacgaggaauuccuaguaagcgcaag
ucaucagcuugcguugauuacgucccugcccuuuguacacaccgcccguc
gcuaguaccgauugaauggcuuagugaggccucaggaucugcuuagagau
cagagcggagaauuuggacaaacuuggucauuuagaggaacuaaaagucg
uaacaagguuuccguaggugaaccugcggaaggaucau

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

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): W7 F8 S9 H10 R12 Y14 G15 K16 G17 R19 C24 G29 L30 I31 R32 K33 Y34 R40 Q41 R44 E45 K54 F55 R56
• Binding residue (residue number reindexed from 1): W4 F5 S6 H7 R9 Y11 G12 K13 G14 R16 C21 G26 L27 I28 R29 K30 Y31 R37 Q38 R41 E42 K51 F52 R53

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P41057|RS29A_YEAST Small ribosomal subunit protein uS14A (Gene Name=RPS29A)