Structure of PDB 8ifd Chain 3H Binding Site BS01

Receptor Information

>8ifd Chain 3H (length=237) Species: 9606 (Homo sapiens)

MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVV
RISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGC
IVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKE
DDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTK
KNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Ligand information

>8ifd Chain 2m (length=1742)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgccgcc
ucucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaa
gcaggcccgagccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcgguc
ggcgucccccaacuucuuagagggacaaguggcguucagccacccgagau
ugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgc
gcuacacugacuggcucagcgugugccuacccuacgccggcaggcgcggg
uaacccguugaaccccauucgugauggggaucggggauugcaauuauucc
ccaugaacgaggaauucccaguaagugcgggucauaagcuugcguugauu
aagucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugg
uuuagugaggcccucggaucggccccgccggggucggcccacggcccugg
cggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagu
cguaacaagguuuccguaggugaaccugcggaaggaucauua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ifd Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): K2 N4 Q13 L15 R31 S53 N56 K58 Q59 G60 F61 P62 Q65 G66 V67 R74 L75 C83 Y84 R87 R88 G90 R92 R94 S96 V108 N110 V112 R131 L133 G134 P135 K136 R137 S139 R140 R154 R159 L162 K164 K167 R170 K172 A173 P174 K175 I176 Q177 R178 V180 R183 Q186 H187 K188 R189 R190 R191 A193 K195 K196 R198 T199 N202 R231 S236 L237
• Binding residue (residue number reindexed from 1): K2 N4 Q13 L15 R31 S53 N56 K58 Q59 G60 F61 P62 Q65 G66 V67 R74 L75 C83 Y84 R87 R88 G90 R92 R94 S96 V108 N110 V112 R131 L133 G134 P135 K136 R137 S139 R140 R154 R159 L162 K164 K167 R170 K172 A173 P174 K175 I176 Q177 R178 V180 R183 Q186 H187 K188 R189 R190 R191 A193 K195 K196 R198 T199 N202 R231 S236 L237

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019901 protein kinase binding

Biological Process

• GO:0000082 G1/S transition of mitotic cell cycle
• GO:0000278 mitotic cell cycle
• GO:0001890 placenta development
• GO:0002181 cytoplasmic translation
• GO:0002309 T cell proliferation involved in immune response
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006924 activation-induced cell death of T cells
• GO:0007369 gastrulation
• GO:0008284 positive regulation of cell population proliferation
• GO:0022605 mammalian oogenesis stage
• GO:0031929 TOR signaling
• GO:0033077 T cell differentiation in thymus
• GO:0042274 ribosomal small subunit biogenesis
• GO:0042593 glucose homeostasis
• GO:0043065 positive regulation of apoptotic process
• GO:0043066 negative regulation of apoptotic process
• GO:0048821 erythrocyte development

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 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:0030425 dendrite
• GO:0032040 small-subunit processome
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0044297 cell body
• GO:0048471 perinuclear region of cytoplasm
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ifd, PDBe:8ifd, PDBj:8ifd
• PDBsum: 8ifd
• PubMed: 38227611
• UniProt: P62753|RS6_HUMAN Small ribosomal subunit protein eS6 (Gene Name=RPS6)