Structure of PDB 6ppk Chain F Binding Site BS01

Receptor Information

>6ppk Chain F (length=139) Species: 1423 (Bacillus subtilis)

NRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVSAVEELTFIAG
QKPVVTRAKGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKKSF
DGRGNYTLGIVRGMDIVIVTTANTDEEARELLTQVGMPF

Ligand information

>6ppk Chain A (length=2658)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacacgugaaauuccgucggaaucc
gggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaac
caguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagag
auccugaaaccgugugccuacaaguagucagagcccguuaacgggugaug
gcgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguua
agcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcauga
guacguggucguagacccgaaaccaggugaucuacccauguccaggguga
aguucagguaacacugaauggaggcccgaacccacgcacguugaaaagug
cggggaugagguguggguaggggugaaaugccaaucgaaccuggagauag
cugguucucuccgaaauagcuuuagggcuagccucaagguaagagucuug
gagguagagcacugauuggacuaggggcgaauucagucaaacuccgaaug
ccaaugacuuauccuugggagucagacugcgagugauaagauccguaguc
gaaagggaaacagcccagaccgccagcuaaggucccaaaguauacguuaa
guggaaaaggauguggaguugcuuagacaaccaggauguugaguuuaaag
aggcucacuggucgagugacucugcgccgaaaauguaccggggcuaaacg
uaucaccgaagcugcggacuguucgaacagugguaggagagcguucuaag
ggcugugaagccagaccggaaggacugguggagcgcuuagaagugagaau
gccgguaugaguagcgaaagaggggugagaauccccuccaccgaaugccu
aagguuuccugaggaaggcucguccgcucaggguuagucgggaccuaagc
cgaggccgaaaggcguaggcgauggacaacagguugauauuccuguacca
ccuccucaccauuugagcaauggggggacgcaggaggauaggguaagcgc
gguauuggauauccgcguccaagcaguuaggcugggaaauaggcaaaucc
guuucccauaaggcugagcugugauggcgagcgaaauauaguagcgaagu
uccugauuccacacugccaagaaaagccucuagcgaggugagaggugccc
guaccgcaaaccgacacagguaggcgaggagagaauccuaaggugaucga
gagaacucucguuaaggaacucggcaaaaugaccccguaacuucgggaga
aggggugcucuguuagggugcaagcccgagagagccgcagugaauaggcc
caggcgacuguuuagcaaaaacacaggucucugcgaagccguaaggcgaa
guauaggggcugacgccaggcgcaacgaucugggcacugucucaacgaga
gacucggugaaauuauaguaccugugaagaugcagguuacccgcgacagg
acggaaccccguggagcuuuacugcagccugauauugaauguugguacag
cuuggauagguaggagccuuggaaaccggaggcuucgguggaggcaucgg
gauacuacccuguauugaccuucuaacccgccgcccuuaucgggcgggga
gacagugucaggugggcaguuugacgggcggucgccuccuaaaagguaac
ggaggcgcccaaagguucccucagaaugguuggaaaucauucgcagagug
uaaaggcacaagggagcuugacugcgagaccuacaagucgagcagggacg
aaagucgggcuuagugauccggugguuccgcauggaagggccaucgcuca
acggauaaaagcuaccccgggcggcucaucgcauccuggggcuguagucg
gucccaaggguugggcuguucgcccauuaaagcgguacgcgagcuggcag
aacgucgugagacaguucggucccuauccgucgcgggcgcaggaaauuug
agaggagcuguccuuaguacgagaggaccgggauggacgcaccgcuggug
uaccaguuguucugccaagggcaucgcuggguagcuaugugcggacggga
uaagugcugaaagcaucuaagcaugaagccccccucaagaugagauuucc
cauuccgcaaggaaguaagaucccugaaagaugaucagguugauaggucu
gagguggaaguguggcgacacauggagcugacagauacuaaucgaucgag
gacuuaac

<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<<<<.....((.>>>.....<<<<<<<..<<<)).....>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<<.....<.....
.>......>>>>>.>...[.....<<....>>...<<<<......<<...
..>>.....>>>>...(((....<<<<<<........>>>>>>......<
<<<<<<<<.....<<<<.......<<<<<<<<<<.<<<.....<<<<...
...>>>>.((......<<<.....))>>>...>>>...>>>>>>>>>>>>
>>.>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......
<<<<<..<<<<>>>>>..)))....].]].>>>>>>>.]]..........
.....<<....>>....]].........<<<<....>>>>..........
........>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>
>>...<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<..
.<<<.....>>>...>>>...<<....>>..<<<<.....>>>>......
>>>>>.>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<......>>>>>>.....>>>...<<<.<<<<<........>>>
>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>......
>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<
<.....<<<...<<<<<<<.............>>>>>>>..>>.>.....
>>>>.>>>>>..>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>
....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<...
........<<..<<<<<<<.<...........<.................
........>.......>.>>>>>>>.>>...........))).....>>>
>>>.>>>...>>>>>>><<<<<<..>>>>>>....>>>>>>..<<<<<<<
.<<......<<<<<.<<....>>.>>>>>...>>.>>>>>>>........
>>>>>><......<<....<<<<<<.......>>>>>><<<<....<<<<
<.<<<..<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<
<...<<<....>>>...>>>...>>...<<<<..........>>>>))<<
<<<.<<<<<<......<<...<<<<....<<<<..<<<..<<<.<.<<<.
......{......>>>.<...<....<.<<.<.<<<<<<<.<<.....>>
>>>>>>>....>.>>..>...>....><..<<...........>>...>>
.>>>...>>>...>>>>.........>>>.>.>>..>>>>>>>>>>>>>>
>.>>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<
<....<<<<<<<<.<<<........<.....<<<<<..............
.>>>>><<<<<....<<<<....>>>>...>>>>>............<<<
<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>...
....>>>>>>>..<<<...>>>...>>.>>>>>>>..>.>>>.>>>>>>>
>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.((
(.[[...<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<<...<.<<<<<<
...........<<...<.........<.<<....>>.>.....>......
....>>...>>>>>>.>...>>>....<<.<<<<<<.....>>>>>>>>.
....>>>>>>>>>..>>>>>..<<.......>><<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<.
...>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>>>....
.........>>>>..]]>>>>.<<<.<.<<<<..<<<<<<<.<......>
.>>>>>..>>.<<<<<.....>>>>>.....>>>>...>...>>>....<
<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<..
.<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<.
..<<<<<<<<<<..}...>>>>>..>>>>>...>>>>.>>>>>...<<<.
<..<<<<<...........>>>>>...>>>>.>>>>.......>>>>>>>
..<<<......>>>....<<<<<<<<<.......>>>>>....<<<<<<<
<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>...
.>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ppk Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.
• Resolution: 4.4 Å
• Binding residue (original residue number in PDB): K33 V35 N37 M38 G39 V40 T68 I85 K88 D123 T129 G151 D153
• Binding residue (residue number reindexed from 1): K32 V34 N36 M37 G38 V39 T56 I63 K66 D101 T107 G113 D115

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ppk, PDBe:6ppk, PDBj:6ppk
• PDBsum: 6ppk
• PubMed: 31665744
• UniProt: P12877|RL5_BACSU Large ribosomal subunit protein uL5 (Gene Name=rplE)