Structure of PDB 8k2d Chain Se Binding Site BS01

Receptor Information

>8k2d Chain Se (length=60) Species: 4932 (Saccharomyces cerevisiae)

AKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVN
GKRRMNPGPS

Ligand information

>8k2d Chain C2 (length=1700)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaaauacagugaaacugcgaauggcucauua
aaucaguuaucguuuauuugauaguuccucuacaugguauaacuguggua
auucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagaugua
uuuauuagauaaaaaaucaaugucuucggacucuuugaugauucauaaua
acuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauuucu
gcccuaucaacuuucgaugguaggauaguggccuaccaugguuucaacgg
guaacggggaauaaggguucgauuccggagagggagccugagaaacggcu
accacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauuca
gggagguagugacaauaaauaacgauacagggucuuguaauuggaaugag
uacaauguaaauaccuuaacgaggaacaauuggagggcaagucuggugcc
agcagccgcgguaauuccagcuccaauagcguauauuaaaguuguugcag
uuaaaaagcucguaguugaacuuugggcccgguuaacggggccuuuccuu
cuggcuaaaccaggacuuuuacuuugaaaaaauuagaguguucaaagcag
gcguauugcucgaauauauuagcauggaauaauagaauaggacguuuggu
ucuauuuuguugguuucuaggaccaucguaaugauuaauagggacggucg
ggggcaucaguauucaauugucagaggugaaauucuuggauuuauugaag
acuaacuacugcgaaagcauuugccaaggacguuuucauuaaucaagaac
gaaaguuaggggaucgaagaugaucagauaccgucguagucuuaaccaua
aacuaugccgacuagggaucgggugguguuuuuuuaaugacccacucggc
accuuacgagaaaucaaagucuuuggguucuggggggaguauggucgcaa
ggcugaaacuuaaaggaauugacggaagggcaccaccaggaguggagccu
gcggcuuaauuugacucaacacggggaaacucaccagguccagacacaau
aaggauugacagauugagagcucuuucuugauuuugugggugguggugca
uggccguucuuaguugguggagugauuugucugcuuaauugcgauaacga
acgagaccuuaaccuacuaaauaguggugcuagcauuugcugguuaucca
cuucuuagagggacuaucgguuucaagccgauggaaguuugaggcaauaa
caggucugugaugcccuuagacguucugggccgcacgcgcgcuacacuga
cggagccagcgagucuaaccuuggccgagaggucuugguaaucuugugaa
acuccgucgugcuggggauagagcauuguaauuauugcucuucaacgagg
aauuccuaguaagcgcaagucaucagcuugcguugauuacgucccugccc
uuuguacacaccgcccgucgcuaguaccgauugaauggcuuagugaggcc
ucaggaucugcagagcggagaauuuggacaaacuuggucauuuagaggaa
cuaaaagucguaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8k2d Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): K3 V4 R10 K13 V14 K15 T18 V21 K23 T24 K26 K28 K31 R33 R37 R43 N46 R55 M56 N57 P58 G59 P60
• Binding residue (residue number reindexed from 1): K2 V3 R9 K12 V13 K14 T17 V20 K22 T23 K25 K27 K30 R32 R36 R42 N45 R54 M55 N56 P57 G58 P59

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0010494 cytoplasmic stress granule
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2d, PDBe:8k2d, PDBj:8k2d
• PDBsum: 8k2d
• PubMed: 38942792
• UniProt: P0CX33|RS30A_YEAST Small ribosomal subunit protein eS30A (Gene Name=RPS30A)