Structure of PDB 6ppf Chain Z Binding Site BS01

Receptor Information

>6ppf Chain Z (length=58) Species: 1423 (Bacillus subtilis)

AKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVS
HLVSVKEQ

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): R10 S11 I13 P16 E17 R20 T22 R24 T25 K29 K30 T31 A42 G45 M46 K49
• Binding residue (residue number reindexed from 1): R9 S10 I12 P15 E16 R19 T21 R23 T24 K28 K29 T30 A41 G44 M45 K48

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ppf, PDBe:6ppf, PDBj:6ppf
• PDBsum: 6ppf
• PubMed: 31665744
• UniProt: P19947|RL30_BACSU Large ribosomal subunit protein uL30 (Gene Name=rpmD)