Structure of PDB 6ppk Chain d Binding Site BS01

Receptor Information
>6ppk Chain d (length=43) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA
Ligand information
>6ppk Chain A (length=2658) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
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(.[[...<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<<...<.<<<<<<
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[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<.
...>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>>>....
.........>>>>..]]>>>>.<<<.<.<<<<..<<<<<<<.<......>
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..<<<<<<<<<<..}...>>>>>..>>>>>...>>>>.>>>>>...<<<.
<..<<<<<...........>>>>>...>>>>.>>>>.......>>>>>>>
..<<<......>>>....<<<<<<<<<.......>>>>>....<<<<<<<
<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>...
.>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ppk Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate.
Resolution4.4 Å
Binding residue
(original residue number in PDB)
R3 T4 F5 Q6 P7 N8 N9 R10 K11 R12 S13 K14 V15 H16 G17 F18 R19 R21 K25 N26 A32 R33 R34 R35 R36 K37 R39 K40 L42
Binding residue
(residue number reindexed from 1)
R2 T3 F4 Q5 P6 N7 N8 R9 K10 R11 S12 K13 V14 H15 G16 F17 R18 R20 K24 N25 A31 R32 R33 R34 R35 K36 R38 K39 L41
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6ppk, PDBe:6ppk, PDBj:6ppk
PDBsum6ppk
PubMed31665744
UniProtP05647|RL34_BACSU Large ribosomal subunit protein bL34 (Gene Name=rpmH)

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