Structure of PDB 6ppf Chain J Binding Site BS01

Receptor Information

>6ppf Chain J (length=141) Species: 1423 (Bacillus subtilis)

TPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGD
HVIIINAEKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLE
LAIKGMLPKGSLGRQMFKKLNVYRGSEHPHEAQKPEVYELR

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): P5 R14 G27 R28 S31 R38 K40 H48 T66 K69 K73 Y76 R77 H78 H81 L85 K86 R88 A105 M109 K112 S114 L115 K121 A135 Q136 K137
• Binding residue (residue number reindexed from 1): P2 R11 G24 R25 S28 R35 K37 H45 T63 K66 K70 Y73 R74 H75 H78 L82 K83 R85 A102 M106 K109 S111 L112 K118 A132 Q133 K134

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• 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: P70974|RL13_BACSU Large ribosomal subunit protein uL13 (Gene Name=rplM)