Structure of PDB 6qik Chain Q Binding Site BS01

Receptor Information

>6qik Chain Q (length=185) Species: 4932 (Saccharomyces cerevisiae)

GIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKA
LFLSKINRPPVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTV
AALRFTAGARAKIVKAGGECITLDQLAVRAPKGQNTLILRGPRNSREAVR
HFGMGPHKGKAPRILSTGRKFERARGRRRSKGFKV

Ligand information

>6qik Chain A (length=3146)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
cgaucaacuuagaacugguacggacaaggggaaucugacugucuaauuaa
aacauagcauugcgauggucagaaagugauguugacgcaaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaccaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggauuaacgagauucccacugucccuauc
uacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcg
gggaaagaagacccuguugagcuugacucuaguuugacauugugaagaga
cauagaggguguagaauaagugggagcuucggcgccagugaaauaccacu
accuuuauaguuucuuuacuuauucaaugaagcggagacguucuagcauu
caaggucccauucggggcugauccggguugaagacauugucaggugggga
guuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagg
ggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccc
ccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccuau
cgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguuac
cacagggauaacuggcuuguggcagucaagcguucauagcgacauugcuu
uuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucggu
aagcguuggauuguucacccacuaauagggaacgugagcuggguuuagac
cgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauag
uaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuug
cggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaugg
cugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugc
uccacacaauauagauggauacgaauaaggcguccuuguggcgucgcuga
accauagcaggcuacgaauugcaaugucauuuugcguggggauaaaucau
uuguauacgacuuagauguacaacgggguauuguaagcaguagaguagcc
uuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qik Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): G2 H5 T6 S7 K8 Q9 H10 K11 R12 S13 G14 H15 R16 K20 S21 K27 K31 R38 P43 S55 K56 I57 S65 R66 R69 Q73 E74 T86 T88 D89 D90 R92 I93 T107 T137 I139 R141 P143 R144 N145 S146 R147 E148 R151 F153 P157 A162 R164 S167 R170 K171 R179 R180 S181 K182
• Binding residue (residue number reindexed from 1): G1 H4 T5 S6 K7 Q8 H9 K10 R11 S12 G13 H14 R15 K19 S20 K26 K30 R37 P42 S54 K55 I56 S64 R65 R68 Q72 E73 T85 T87 D88 D89 R91 I92 T106 T136 I138 R140 P142 R143 N144 S145 R146 E147 R150 F152 P156 A161 R163 S166 R169 K170 R178 R179 S180 K181

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6qik, PDBe:6qik, PDBj:6qik
• PDBsum: 6qik
• PubMed: 31115337
• UniProt: P0CX49|RL18A_YEAST Large ribosomal subunit protein eL18A (Gene Name=RPL18A)