Structure of PDB 5lks Chain SI Binding Site BS02

Receptor Information

>5lks Chain SI (length=206) Species: 9606 (Homo sapiens)

GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGG
NKKYRALRLDVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCI
VLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSKKIQKKYDE
RKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
IKARKG

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): G2 R5 H9 K10 R11 R12 G15 G16 K19 Y21 K23 K24 R25 K26 Y27 G30 R31 A33 R41 R42 T45 R47 R49 K53 K54 Y55 R56 L58 N64 S66 C71 C72 T73 R74 K75 N87 V97 K98 N99 K140 R141 K143 K144 I145 A176 R178 Q181 R184
• Binding residue (residue number reindexed from 1): G1 R4 H8 K9 R10 R11 G14 G15 K18 Y20 K22 K23 R24 K25 Y26 G29 R30 A32 R40 R41 T44 R46 R48 K52 K53 Y54 R55 L57 N63 S65 C70 C71 T72 R73 K74 N86 V96 K97 N98 K139 R140 K142 K143 I144 A175 R177 Q180 R183

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:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

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:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5lks, PDBe:5lks, PDBj:5lks
• PDBsum: 5lks
• PubMed: 27665925
• UniProt: P62241|RS8_HUMAN Small ribosomal subunit protein eS8 (Gene Name=RPS8)