Structure of PDB 8k2c Chain Sa Binding Site BS01

Receptor Information

>8k2c Chain Sa (length=102) Species: 9606 (Homo sapiens)

TKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVR
DISEASVFDAYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRF
RP

Ligand information

>8k2c Chain S2 (length=1740)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgcccuc
ucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaagc
aggcccgagccgccuggauaccgcagcuaggaauaauggaauaggaccgc
gguucuauuuuguugguuuucggaacugaggccaugauuaagagggacgg
ccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcgc
aagacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaag
aacgaaagucggagguucgaagacgaucagauaccgucguaguuccgacc
auaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgccg
ggcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguug
caaagcugaaacuuaaaggaauugacggaagggcaccaccaggaguggag
ccugcggcuuaauuugacucaacacgggaaaccucacccggcccggacac
ggacaggauugacagauugauagcucuuucucgauuccgugggugguggu
gcauggccguucuuaguugguggagcgauuugucugguuaauuccgauaa
cgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucgg
cgucccccaacuucuuagagggacaaguggcguucagccacccgagauug
agcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcgc
uacacugacuggcucagcgugugccuacccuacgccggcaggcgcgggua
acccguugaaccccauucgugauggggaucggggauugcaauuauucccc
augaacgaggaauucccaguaagugcgggucauaagcuugcguugauuaa
gucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguu
uagugaggcccucggaucggccccgccggggucggcccacggcccuggcg
gagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagucg
uaacaagguuuccguaggugaaccugcggaaggaucauua

...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<..................<<.....
<<.<<<.....>>>.>>......>>.........<<<<...<<<<<....
.>.>>>>...>>>><<..<<<<<...<......>..>>>>>......>>.
..<<<<.<<<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<....>>.>...>>>>>>.........<<<....<<<<...>>>>..>>>
..>...>>.>.....<<<<<<<<<.<<<....>>>..>>>>>.>>>>...
...<<..<...........>..>>.........<<<<<((......<<<<
.....<<..))>>.......>>>>.>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<.<<.......................<<.
<.............>>>...<<<<<<.<.......<<...<.......>.
<<<<.......>>>>...>>......>.>>>..>>>........<.<<.<
<<<<<<...............>>>>>>>.>>.>....>>....<<<<<<.
.<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>>>
>>..>>.......<<....>>...>>>>..>..>>>.>>>...>>>...>
>.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>.
.........<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>>>
.>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<<.
...>>>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..<<
<.<<<<<<......<<........>>..........<<<<<.<....<<<
<<<.......<<.<<<........>>>.>>.....>>>>>>...<<.<<<
..<<.<<<<<<....<<<.<<<<<....>>>...<<<......>>>...>
>.>>>....<<<...<...<<<<..<<<<<<<<<<<<.......>>>>.>
>>>.....>>>>..>>>>..>.....<<<<<.....>>>>>........>
>>....>>>.>>>.....>>>>>>>.....>.>>>>>...>>.>>>>.>>
>.....<<.<<<........<.......<<<.<<<<....>>>>.>>>..
..>.........>>>.>>......<.....<<<<<..........>>>>>
.....>.....>>>>>.....<<<<<<<<.......>>>>>>>>......
>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<
.<<<..<<<<.<<...<<<<<...<<<...................>>>.
....>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.>>
...>.....<<<<<<<<<<..>>>>>>>>>>.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8k2c Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): T2 K3 K4 R5 R6 N7 N8 G9 R10 K13 G14 R15 G16 H17 R28 K32 K34 K37 K38 F39 K70 V75 S76 I79 H80 K82 V83 V84 R85 N86 R87 S88 R89 R92 R95 P97 P98
• Binding residue (residue number reindexed from 1): T1 K2 K3 R4 R5 N6 N7 G8 R9 K12 G13 R14 G15 H16 R27 K31 K33 K36 K37 F38 K69 V74 S75 I78 H79 K81 V82 V83 R84 N85 R86 S87 R88 R91 R94 P96 P97

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0033119 negative regulation of RNA splicing

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:0098556 cytoplasmic side of rough endoplasmic reticulum membrane
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2c, PDBe:8k2c, PDBj:8k2c
• PDBsum: 8k2c
• PubMed: 38942792
• UniProt: P62854|RS26_HUMAN Small ribosomal subunit protein eS26 (Gene Name=RPS26)