Structure of PDB 6ppk Chain T Binding Site BS01

Receptor Information

>6ppk Chain T (length=90) Species: 1423 (Bacillus subtilis)

DPRDVLKRPVITERSADLMTEKKYTFEVDVRANKTEVKDAVESIFGVKVD
KVNIMNYKGKSKRVGRYTGMTSRRRKAIVKLTADSKEIEI

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

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.<<<<<<.....((.>>>.....<<<<<<<..<<<)).....>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<<.....<.....
.>......>>>>>.>...[.....<<....>>...<<<<......<<...
..>>.....>>>>...(((....<<<<<<........>>>>>>......<
<<<<<<<<.....<<<<.......<<<<<<<<<<.<<<.....<<<<...
...>>>>.((......<<<.....))>>>...>>>...>>>>>>>>>>>>
>>.>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......
<<<<<..<<<<>>>>>..)))....].]].>>>>>>>.]]..........
.....<<....>>....]].........<<<<....>>>>..........
........>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>
>>...<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<..
.<<<.....>>>...>>>...<<....>>..<<<<.....>>>>......
>>>>>.>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<......>>>>>>.....>>>...<<<.<<<<<........>>>
>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>......
>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<
<.....<<<...<<<<<<<.............>>>>>>>..>>.>.....
>>>>.>>>>>..>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>
....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<...
........<<..<<<<<<<.<...........<.................
........>.......>.>>>>>>>.>>...........))).....>>>
>>>.>>>...>>>>>>><<<<<<..>>>>>>....>>>>>>..<<<<<<<
.<<......<<<<<.<<....>>.>>>>>...>>.>>>>>>>........
>>>>>><......<<....<<<<<<.......>>>>>><<<<....<<<<
<.<<<..<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<
<...<<<....>>>...>>>...>>...<<<<..........>>>>))<<
<<<.<<<<<<......<<...<<<<....<<<<..<<<..<<<.<.<<<.
......{......>>>.<...<....<.<<.<.<<<<<<<.<<.....>>
>>>>>>>....>.>>..>...>....><..<<...........>>...>>
.>>>...>>>...>>>>.........>>>.>.>>..>>>>>>>>>>>>>>
>.>>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<
<....<<<<<<<<.<<<........<.....<<<<<..............
.>>>>><<<<<....<<<<....>>>>...>>>>>............<<<
<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>...
....>>>>>>>..<<<...>>>...>>.>>>>>>>..>.>>>.>>>>>>>
>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.((
(.[[...<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<<...<.<<<<<<
...........<<...<.........<.<<....>>.>.....>......
....>>...>>>>>>.>...>>>....<<.<<<<<<.....>>>>>>>>.
....>>>>>>>>>..>>>>>..<<.......>><<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<.
...>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>>>....
.........>>>>..]]>>>>.<<<.<.<<<<..<<<<<<<.<......>
.>>>>>..>>.<<<<<.....>>>>>.....>>>>...>...>>>....<
<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<..
.<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<.
..<<<<<<<<<<..}...>>>>>..>>>>>...>>>>.>>>>>...<<<.
<..<<<<<...........>>>>>...>>>>.>>>>.......>>>>>>>
..<<<......>>>....<<<<<<<<<.......>>>>>....<<<<<<<
<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>...
.>>>>>>.

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): T14 R16 K25 N35 K36 T37 K40 K53 N55 I56 M57 N58 K60 K62 K64 V66 Y69 G71 S74 R75 R77 K78 K82
• Binding residue (residue number reindexed from 1): T12 R14 K23 N33 K34 T35 K38 K51 N53 I54 M55 N56 K58 K60 K62 V64 Y67 G69 S72 R73 R75 K76 K80

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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: P42924|RL23_BACSU Large ribosomal subunit protein uL23 (Gene Name=rplW)