Structure of PDB 5ndg Chain D7 Binding Site BS01

Receptor Information

>5ndg Chain D7 (length=81) Species: 4932 (Saccharomyces cerevisiae)

VLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQ
TAVTCESCSTILCTPTGGKAKLSEGTSFRRK

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): R17 H19 K20 L21 K22 P28 S30 F32 F47 H49 Q51 T67 G68 G69 K70 K72
• Binding residue (residue number reindexed from 1): R16 H18 K19 L20 K21 P27 S29 F31 F46 H48 Q50 T66 G67 G68 K69 K71

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0046872 metal ion 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:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndg, PDBe:5ndg, PDBj:5ndg
• PDBsum: 5ndg
• PubMed: 29208708
• UniProt: P35997|RS27A_YEAST Small ribosomal subunit protein eS27A (Gene Name=RPS27A)