Structure of PDB 6ppk Chain D Binding Site BS01

Receptor Information

>6ppk Chain D (length=206) Species: 1423 (Bacillus subtilis)

TKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQL
GFDDKREKLSNKPEKGHVAKAETAPKRFVKELRGVEMDAYEVGQEVKVEI
FSAGEIVDVTGVSKGKGFQGAIKRHGQSRGPMSHGSRYHRRPGSMGPVDP
NRVFKGKLLPGRMGGEQITVQNLEIVKVDAERNLLLIKGNVPGAKKSLIT
VKSAVK

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): M12 Q14 P24 Q37 K39 D44 Y46 R57 K59 L60 N62 K63 P64 G67 K71 V80 E82 R84 K115 G116 K117 G118 F119 G121 I123 K124 R125 Q128 S129 R130 M133 S134 H135 S137 R138 Y139 H140 R141 P143 S145 M146 P148 V149 D150 N152 R153 V154 K156 G157 L160 R163 Q168 I169 T170 Q172 N173 L174 K189 G190 N191 P193 K197 K207
• Binding residue (residue number reindexed from 1): M11 Q13 P23 Q36 K38 D43 Y45 R56 K58 L59 N61 K62 P63 G66 K70 V79 E81 R83 K114 G115 K116 G117 F118 G120 I122 K123 R124 Q127 S128 R129 M132 S133 H134 S136 R137 Y138 H139 R140 P142 S144 M145 P147 V148 D149 N151 R152 V153 K155 G156 L159 R162 Q167 I168 T169 Q171 N172 L173 K188 G189 N190 P192 K196 K206

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:6ppk, PDBe:6ppk, PDBj:6ppk
• PDBsum: 6ppk
• PubMed: 31665744
• UniProt: P42920|RL3_BACSU Large ribosomal subunit protein uL3 (Gene Name=rplC)