Structure of PDB 5lks Chain SQ Binding Site BS01

Receptor Information

>5lks Chain SQ (length=146) Species: 9606 (Homo sapiens)

MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYK
LLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYV
DEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR

Ligand information

>5lks Chain S2 (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: 5lks Structure-function insights reveal the human ribosome as a cancer target for antibiotics.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): M1 K4 S9 Q11 V12 F13 R15 K16 K17 T18 A23 H24 K33 G36 R69 R71 G74 G75 G76 H77 V78 A79 R125 R126 C127 E128 S129 K130 K131 F132 G136 A137 R138 A139 R140 Y141 Q142 K143 S144 Y145 R146
• Binding residue (residue number reindexed from 1): M1 K4 S9 Q11 V12 F13 R15 K16 K17 T18 A23 H24 K33 G36 R69 R71 G74 G75 G76 H77 V78 A79 R125 R126 C127 E128 S129 K130 K131 F132 G136 A137 R138 A139 R140 Y141 Q142 K143 S144 Y145 R146

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis
• GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5lks, PDBe:5lks, PDBj:5lks
• PDBsum: 5lks
• PubMed: 27665925
• UniProt: P62249|RS16_HUMAN Small ribosomal subunit protein uS9 (Gene Name=RPS16)