Structure of PDB 8g6j Chain SG Binding Site BS01

Receptor Information

>8g6j Chain SG (length=237) Species: 9606 (Homo sapiens)

MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVV
RISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGC
IVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKE
DDVRQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTK
KNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Ligand information

>8g6j Chain S2 (length=1701)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgccacuuggauaacuguggua
auucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggg
augcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcac
gccccccguggcggcgacgacccauucgaacgucugcccuaucaacuuuc
gaugguagucgccgugccuaccauggugaccacgggugacggggaaucag
gguucgauuccggagagggagccugagaaacggcuaccacauccaaggaa
ggcagcaggcgcgcaaauuacccacucccgacccggggagguagugacga
aaaauaacaauacaggacucuuucgaggcccuguaauuggaaugagucca
cuuuaaauccuuuaacgaggauccauuggagggcaagucuggugccagca
gccgcgguaauuccagcuccaauagcguauauuaaaguugcugcaguuaa
aaagcucguaguuggaucuugggagcgggcguccccgccuuuacuuugaa
aaaauuagaguguucaaagcaggcccgagccgccuggauaccgcagcuag
gaauaauggaauaggaccgcgguucuauuuuguugguuuucggaacugag
gccaugauuaagagggacggccgggggcauucguauugcgccgcuagagg
ugaaauucuuggaccggcgcaagacggaccagagcgaaagcauuugccaa
gaauguuuucauuaaucaagaacgaaagucggagguucgaagacgaucag
auaccgucguaguuccgaccauaaacgaugccgaccggcgaugcggcggc
guuauucccaugacccgccgggcagcuuccgggaaaccaaagucuuuggg
uuccggggggaguaugguugcaaagcugaaacuuaaaggaauugacggaa
gggcaccaccaggaguggagccugcggcuuaauuugacucaacacgggaa
accucacccggcccggacacggacaggauugacagauugauagcucuuuc
ucgauuccgugggugguggugcauggccguucuuaguugguggagcgauu
ugucugguuaauuccgauaacgaacgagacucuggcaugcuaacuaguua
cgcgacccccgagcggucggcgucccccaacuucuuagagggacaagugg
cguucagccacccgagauugagcaauaacaggucugugaugcccuuagau
guccggggcugcacgcgcgcuacacugacuggcucagcgugugccuaccc
uacgccggcaggcgcggguaacccguugaaccccauucgugauggggauc
ggggauugcaauuauuccccaugaacgaggaauucccaguaagugcgggu
cauaagcuugcguugauuaagucccugcccuuuguacacaccgcccgucg
cuacuaccgauuggaugguuuagugaggcccucggaucggccccgccggg
gugcccuggcggagcgcugagaagacggucgaacuugacuaucuagagga
aguaaaagucguaacaagguuuccguaggugaaccugcggaaggaucauu
a

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g6j mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): N4 S6 Q13 L15 R31 S53 N56 K58 Q59 G60 F61 P62 Q65 G66 R72 R74 L75 H81 C83 Y84 R85 R87 R88 G90 E91 R92 R94 K95 S96 S107 V108 N110 V112 R131 R132 L133 G134 K136 R137 S139 R140 K143 K149 R154 R159 K160 L162 N163 K164 K167 K168 R170 T171 K172 A173 P174 K175 I176 Q177 R178 V180 R183 V184 Q186 H187 R189 R190 R191 I192 K195 K196 R198 T199 K201 N202
• Binding residue (residue number reindexed from 1): N4 S6 Q13 L15 R31 S53 N56 K58 Q59 G60 F61 P62 Q65 G66 R72 R74 L75 H81 C83 Y84 R85 R87 R88 G90 E91 R92 R94 K95 S96 S107 V108 N110 V112 R131 R132 L133 G134 K136 R137 S139 R140 K143 K149 R154 R159 K160 L162 N163 K164 K167 K168 R170 T171 K172 A173 P174 K175 I176 Q177 R178 V180 R183 V184 Q186 H187 R189 R190 R191 I192 K195 K196 R198 T199 K201 N202

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:8g6j, PDBe:8g6j, PDBj:8g6j
• PDBsum: 8g6j
• PubMed: 37020024
• UniProt: P62753|RS6_HUMAN Small ribosomal subunit protein eS6 (Gene Name=RPS6)