Structure of PDB 6ppf Chain P Binding Site BS01

Receptor Information

>6ppf Chain P (length=103) Species: 1423 (Bacillus subtilis)

QKLIEDITKEQLRTDLPAFRPGDTLRVHVKVVEGNRERIQIFEGVVIKRR
GGGISETFTVRKISYGVGVERTFPVHTPKIAKIEVVRYGKVRRAKLYYLR
ELR

Ligand information

>6ppf Chain A (length=2471)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacacgugaaauuccgucggaaucc
gggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaac
caguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagag
auccugaaaccgugugccuacaaguagucagagcccguuaacgggugaug
gcgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguua
agcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcauga
guacguggucguagacccgaaaccaggugaucuacccauguccaggguga
aguucagguaacacugaauggaggcccgaacccacgcacguugaaaagug
cggggaugagguguggguaggggugaaaugccaaucgaaccuggagauag
cugguucucuccgaaauagcuuuagggcuagccucaagguaagagucuug
gagguagagcacugauuggacuagaauucagucaaacuccgaaugccaau
gacuuauccuugggagucagacugcgagugauaagauccguagucgaaag
ggaaacagcccagaccgccagcuaaggucccaaaguauacguuaagugga
aaaggauguggaguugcuuagacaaccaggauguuggcauuuaaagagug
cguaauagcucacuggucgagugacucugcgccgaguaccggggcuaaac
guaucaccgaagcugcggacuguucgaacagugguaggagagcguucuaa
gggcugugaagccagaccggaaggacugguggagcgcuuagaagugagaa
ugccgguaugaguagcgaaagaggggugagaauccccuccaccgaaugcc
uaagguuuccugaggaaggcucguccgcucaggguuagucgggaccuaag
ccgaggccgaaaggcguaggcgauggacaacagguugauauuccuguacc
accuccucaccauuugagcaauggggggacgcaggaggauaggguaagcg
cgguauuggauauccgcguccaagcaguuaggcugggaaauaggcaaauc
cguuucccauaaggcugagcugugauggcgagcgaaauuaguagcgaagu
uccugauuccacacugccaagaaaagccucuagcgaggugagaggugccc
guaccgcaaaccgacacagguaggcgaggagagaauccuaaggugaucga
gagaacucucguuaaggaacucggcaaaaugaccccguaacuucgggaga
aggggugcucuguuagggugcaagcccgagagagccgcagugaauaggcc
caggcgacuguuaaacacaggucucugcgaagccguaaggcgaaguauag
gggcugacgccuggcgcaacgaucugggcacugucucaacgagagacucg
gugaaauuauaguaccugugaaugcagguuacccgcgacaggacggaacc
ccguggagcuuuacugcagccugauauugaaugccuucuaacccgccgcc
cuuaucgggcggggagacagugucaggugggcaguuugacgggcggucgc
cuccuaaaagguaacggaggcgcccaaagguucccucagaaugguuggaa
aucauucgcagaguguaaaggcacaagggagcuugacugcgagaccuaca
agucgagcagggacgaaagucgggcuuagugauccggugguuccgcaugg
aagggccaucgcucaacggauaaaagcuaccccgggcuauccgucgcggg
cgcaggaaauuugagaggagcuguccuuaguacgagaggaccgggaugga
cgcaccgcugguguaccaguuguucugccaagggcaucgcuggguagcua
ugugcggacgggauaagugcugaaagcaucuaagcaugaagccccccuca
agaugagauuucccauuccgcaaggaaguaagaucccugaaagaugauca
gguugauaggucugagguggaaguguggcgacacauggagcugacagaua
cuaaucgaucgaggacuuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ppf Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R24 K52 R54 T61 R96 R97 A98 K99 Y101
• Binding residue (residue number reindexed from 1): R20 K48 R50 T57 R92 R93 A94 K95 Y97

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6ppf, PDBe:6ppf, PDBj:6ppf
• PDBsum: 6ppf
• PubMed: 31665744
• UniProt: O31742|RL19_BACSU Large ribosomal subunit protein bL19 (Gene Name=rplS)