Structure of PDB 6ppf Chain D Binding Site BS01

Receptor Information

>6ppf Chain D (length=167) Species: 1423 (Bacillus subtilis)

KGILGRKIGMTQVFAEDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFD
DKREKLSNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEIFSA
GEIVDVTGVSKGKGFQGALLPGRMGGEQITVQNLEIVKVDAERNLLLIKG
NVPGAKKSLITVKSAVK

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): M12 Q14 P24 Q37 D44 Y46 R57 K59 N62 K63 G67 H68 K71 R78 E82 R84 S114 K115 G116 G118 F119 R163 E167 Q168 T170 Q172 N173 N191 V192 K197
• Binding residue (residue number reindexed from 1): M10 Q12 P20 Q33 D40 Y42 R53 K55 N58 K59 G63 H64 K67 R74 E78 R80 S110 K111 G112 G114 F115 R123 E127 Q128 T130 Q132 N133 N151 V152 K157

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:2000234 positive regulation of rRNA processing

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: P42920|RL3_BACSU Large ribosomal subunit protein uL3 (Gene Name=rplC)