Structure of PDB 6xu7 Chain CD Binding Site BS02

Receptor Information

>6xu7 Chain CD (length=290) Species: 7227 (Drosophila melanogaster)

KNKQYFKRYQVKFRRRREGKTDYYARKRLTFQDKNKYNTPKYRLIVRLSN
KDITVQIAYARIEGDRVVCAAYSHELPKYGIQVGLTNYAAAYCTGLLVAR
RVLNKLGLDSLYAGCTEVTGEEFNVEPVDDGPGAFRCFLDVGLARTTTGA
RVFGAMKGAVDGGLNIPHSVKRFPGYSAETKSFNADVHRAHIFGQHVADY
MRSLEEEDEESFKRQFSRYIKLGIRADDLEDIYKKAHQAIRNDPTHKVTA
KKSSAVTKKRWNAKKLTNEQRKTKIAAHKAAYVAKLQSET

Ligand information

>6xu7 Chain A5 (length=3707)

uuauauacaaccucaacucauaugggacuacccccugaauuuaagcauau
uaauuaggggaggaaaagaaacuaacaaggauuuucuuaguagcggcgag
cgaaaagaaaacaguucagcacuaagucacuuugucuauauggcaaaugu
gagaugcaguguauggagcgucaauauucuaguaugagaaauuaacgauu
uaaguccuucuuaaaugaggccauuuacccauagagggugccaggcccgu
auaacguuaaugauuacuagaugauguuuccaaagagucguguugcuuga
uagugcagcacuaagugggugguaaacuccaucuaaaacuaaauauaacc
augagaccgauaguaaacaaguaccgugagggaaaguugaaaagaacucu
gaauagagaguuaaacaguacgugaaacugcuuagagguuaagcccgaug
aaccugaauauccguuauggaaaauucaucauuaaaauuguaauauuuaa
auaauauuaugagaauagugugcauuuuuuccauauaaggacauuguaau
cuauuagcauauaccaaauuuaucauaaaauauaacuuauaguuuauucc
aauuaaauugcuugcauuuuaacacagaauaaauguuauuaauuugauaa
agugcugauagauuuauaugauuacagugcguuaauuuuucggaauuaua
uaauggcauaauuaucauugauuuuuguguuuauuauaugcacuuguaug
auuaacaaugcgaaagauucaggauaccuucgggacccgucuugaaacac
ggaccaaggagucuaacauaugugcaaguuauugggauauaaaccuaaua
gcguaauuaacuugacuaauaaugggauuaguuuuuuagcuauuuauagc
uaauuaacacaaucccggggcguucuauauaguuauguauaauguauauu
uauauuauuuaugccucuaacuggaacguaccuugagcauauaugcugug
acccgaaagauggugaacuauacuugaucagguugaagucaggggaaacc
cugauggaagaccgaaacaguucugacgugcaaaucgauugucagaauug
aguauaggggcgaaagaccaaucgaaccaucuaguagcugguuccuuccg
aaguuucccucaggauagcuggugcauuuuaauauuauauaaaauaaucu
uaucugguaaagcgaaugauuagaggccuuagggucgaaacgaucuuaac
cuauucucaaacuuuaaauggguaagaaccuuaacuuucuugauaugaag
aucaagguuaugauauaaaugucccagugggccacuuuugguaagcagaa
cuggcgcugugggaugaaccaaacguaauguuacgugcccaaauuaacaa
cucaugcagauaccaugaaaggcguugguugcuuaaaacagcaggacggu
gaucauggaagucgaaauccgcuaaggaguguguaacaacucaccugccg
aagcaacuagcccuuaaaauggauggcgcuuaaguuguauaccuauacau
uaccgcuaaaguagaugauuuauauuacuugugauauaaauuuugaaacu
uuagugaguaggaagguacaaugguaugcguagaaguguuuggcguaagc
cugcauggagcugccauugguacagaucuugguggauaguagcaaauaau
cgaaugagagccuuggaggacugaaguggagaaggguuucgugugaacag
ugguugaucacgaguuagucgguccuaaguucaaggcgaaagcgaaaauu
uucaaguaaaacauaauuuugaacgaaagggaauacgguuccaauuccgu
aaccuguugaguauccguuuguuauuaaauaugggccucgugcucauccu
ggcaacaggaacgaccauaaagaagccgucgagagauaucggaagaguuu
ucuuuucuguuuuauagccguacuaccauggaagucuuucgcagagagau
augguagaugggcuagaagagcaugacauauacuguugugucgauauuuu
cuccucggaccuugaaaauuuaugguggggacacgcaaacuucucaacag
gccguaccaauauccgcagcuggucuccaaggugaagagucucuagucga
uagaauaauguagguaagggaagucggcaaauuagauccguaacuucggg
auaaggauuggcucugaagauugagauagucggccuugauugggaaacug
gaacuuucuugcuaaauuauaacgauuaucaauuaacaaucaauucagaa
cuggcacggacuuggggaauccgacugucuaauuaaaacaaagcauugug
auggcccuagcggguguugacacaaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaguaagcgcgggucaacggcgggaguaacu
augacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgc
augaauggauuaacgagauuccuacugucccuaucuacuaucuagcgaaa
ccacagccaagggaacgggcuuggaauaauuagcggggaaagaagacccu
uuugagcuugacucuaaucuggcaguguaaggagacauaagagguguaga
auaagugggagauauuagaccucgguuugguaucgucaaugaaauaccac
uacucuuauuguuuccuuacuuacuugauuaaauggaacguguaucauuu
ccuagauuggguuuugaugcaagcuucuugaucaaaguaucacgaguuug
uuauauaaucgcaaacaaauuugguauaacuccaauuacucagguaugau
ccaauucaaggacauugccagguagggaguuugacuggggcgguacaucu
cucaaauaauaacggaggugucccaaggccagcucagugcggacagaaac
cacacauagagcaaaagggcaaaugcugacuugaucucgguguucaguac
acacagggacagcaaaagcucggccuaucgauccuuuugguuuaaagagu
uuuuaacaagaggugucagaaaaguuaccauagggauaacuggcuugugg
cggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcuc
uuccuaucauugugaagcaaaauucaccaagcguuggauuguucacccau
gcaagggaacgugagcuggguuuagaccgucgugagacagguuaguuuua
cccuacuaaugacaaaacguuguugcgacagcauuccugcguaguacgag
aggaacccgcagguacggaccaauggcacaauacuuguucgagcgaacag
ugguaugacgcuacguccguuggauuaugccugaacgccucuaaggucgu
auccgugcuggacugcaaugauaaauaaggggcaauuugcauuguauggc
uucuaaaccauuuaaaguuuauaauuuacuuuauaaacgacaauggaugu
gaugccaauguaauuuguaacauaguaaauugggaggaucuucgaucacc
ugaugccgcgcuaguuacauauaaaagcauuauuuaauacaaugacaaag
ccuagaaucaauuguaaacgacuuuuguaacaggcaagguguuguaagug
guugagcagcugccauacugcgauccacugaagcuuauccuuugcuugau
gauucga

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xu7 Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching.
• Resolution: 4.9 Å
• Binding residue (original residue number in PDB): Q11 Y12 R15 Y16 Q17 K19 R23 D29 Y31 R35 L36 F38 K43 Y44 T46 K48 L113 P139 G140 A141 F145 V148 R152 T153 P174 S176 R179
• Binding residue (residue number reindexed from 1): Q4 Y5 R8 Y9 Q10 K12 R16 D22 Y24 R28 L29 F31 K36 Y37 T39 K41 L106 P132 G133 A134 F138 V141 R145 T146 P167 S169 R172

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xu7, PDBe:6xu7, PDBj:6xu7
• PDBsum: 6xu7
• PubMed: 34283226
• UniProt: Q9W5R8|RL5_DROME Large ribosomal subunit protein uL18 (Gene Name=RpL5)