Structure of PDB 6ppk Chain N Binding Site BS01

Receptor Information

>6ppk Chain N (length=118) Species: 1423 (Bacillus subtilis)

YRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGK
RGDLHARRQAAAYIRNEVANEENNQDALQKLFSDIATRYEERQGGYTRIM
KLGPRRGDGAPMAIIELV

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): Y3 R4 K5 R8 S10 A11 Q12 R13 K14 R18 D23 N27 I30 T35 K38 E39 R41 S42 E45 K46 T49 R53 H57 R59 R60 Q61 A64 R67 N68 Q81 R94 Q95 G96 G97 T99 R100 K103 R107 R108 G109 D110 G111 A112
• Binding residue (residue number reindexed from 1): Y1 R2 K3 R6 S8 A9 Q10 R11 K12 R16 D21 N25 I28 T33 K36 E37 R39 S40 E43 K44 T47 R51 H55 R57 R58 Q59 A62 R65 N66 Q79 R92 Q93 G94 G95 T97 R98 K101 R105 R106 G107 D108 G109 A110

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:6ppk, PDBe:6ppk, PDBj:6ppk
• PDBsum: 6ppk
• PubMed: 31665744
• UniProt: P20277|RL17_BACSU Large ribosomal subunit protein bL17 (Gene Name=rplQ)