Structure of PDB 8k82 Chain Sa Binding Site BS01

Receptor Information

>8k82 Chain Sa (length=97) Species: 4932 (Saccharomyces cerevisiae)

PKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVR
DLSEASVYPEYALPKTYNKLHYCVSCAIHARIVRVRSREDRKNRAPP

Ligand information

>8k82 Chain C2 (length=1771)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagggcccauucggguc
uuguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauugga
gggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguau
auuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguu
ggccggucggauuuccaacggggccuuuccuucuggcuaaccuugagcuu
ggcgaaccaggacuuuuacuuugaaaaaauuagaguguucaaagcaggcg
uauugcucgaauauauuagcauggaauaauagaauaggacguuugguucu
auuuuguugguuucuaggaccaucguaaugauuaauagggacggucgggg
gcaucaguauucaauugucagaggugaaauucuuggauuuauugaagacu
aacuacugcgaaagcauuugccaaggacguuuucauuaaucaagaacgaa
aguuaggggaucgaagaugaucagauaccgucguagucuuaaccauaaac
uaugccgacuagggaucgggugguguuuuuuuaaugacccacucggcacc
uuacgagaaaucaaagucuuuggguucuggggggaguauggucgcaaggc
ugaaacuuaaaggaauugacggaagggcaccaccaggaguggagccugcg
gcuuaauuugacucaacacggggaaacucaccagguccagacacaauaag
gauugacagauugagagcucuuucuugauuuugugggugguggugcaugg
ccguucuuaguugguggagugauuugucugcuuaauugcgauaacgaacg
agaccuuaaccuacuaaauaguggugcuagcauuugcugguuauccacuu
cuuagagggacuaucgguuucaagccgauggaaguuugaggcaauaacag
gucugugaugcccuuagacguucugggccgcacgcgcgcuacacugacgg
agccagcgagucuaaccuuggccgagaggucuugguaaucuugugaaacu
ccgucgugcuggggauagagcauuguaauuauugcucuucaacgaggaau
uccuaguaagcgcaagucaucagcuugcguugauuacgucccugcccuuu
guacacaccgcccgucgcuaguaccgauugaauggcuuagugaggccuca
ggaucugcuuagagaagggggcaacuccaucucagagcggagaauuugga
caaacuuggucauuuagaggaacuaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucauu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8k82 Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): P2 K3 K4 R5 A6 S7 N8 G9 R10 N11 K12 K13 R15 G16 H17 K19 K32 K34 K37 R38 K70 V75 S76 I79 V84 R85 V86 R87 S88 R89 R92 K93 R95
• Binding residue (residue number reindexed from 1): P1 K2 K3 R4 A5 S6 N7 G8 R9 N10 K11 K12 R14 G15 H16 K18 K31 K33 K36 R37 K69 V74 S75 I78 V83 R84 V85 R86 S87 R88 R91 K92 R94

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0042255 ribosome assembly

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k82, PDBe:8k82, PDBj:8k82
• PDBsum: 8k82
• PubMed: 38942792
• UniProt: P39939|RS26B_YEAST Small ribosomal subunit protein eS26B (Gene Name=RPS26B)