Structure of PDB 6pvk Chain U Binding Site BS01

Receptor Information

>6pvk Chain U (length=90) Species: 1423 (Bacillus subtilis)

HVKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVEGVNMVKKHSKPGISN
QEAPIHVSNVMPLDPKTGEVTRVGYKVEKVRVAKKSGQVL

Ligand information

>6pvk Chain A (length=2169)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacaaauuccgucggaauccgggag
gaccaucucccaaggcuaaauacucccuagugaccgauagugaaccagua
ccgugagggaaaggugaaaagcaccccggaaggggagugaaagagauccu
gaaaccgugugccuacaaguagucagagcccguuaacgggugauggcgug
ccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguuaagcag
aagaugcggagccgcagcgaaagcgagucugaauagggcgcaugaguacg
uggucguagacccgaaaccaggugaucuacccauguccagggugaaguuc
agguaacacugaauggaggcccgaacccacgcacguugaaaagugcgggg
augagguguggguaggggugaaaugccaaucgaaccuggagauagcuggu
ucucuccgaaauagcuuuaggcuagccucaagguaagagucuugaugcca
augacuuauccuugggagucagacugcgagugauaauccguagucgaaag
ggaaacagcccagaccgccagcuaaggucccaaaguauacguuaagugga
aaaggauguggaguugcuuagacgagugacucugcgccgacggggcuaaa
cguaucaccgaagcugcggacuguucgaacagugguaggagagcguucua
agggcugugaagccagaccggaaggacugguggagcgcuuagaagugaga
augccgguaugaguagcgaaagaggggugagaauccccuccaccgaaugc
cuaagguuuccugaggaaggcucguccgcucaggguuagucgggaccuaa
gccgaggccgaaaggcguaggcgauggacaacagguugauauuccuguac
caccuccucaccauuugagcaauggggggacgcaggaggauaggguaagc
gcgguauuggauauccgcguccaagcaguuaggcugggaaauaggcaaau
ccguuucccauaaggcugagcugugauggcgagcgaaaguagcgaaguuc
cugauuccacacugccaagaaaagccucuagcgaggugagaggugcccgu
accgcaaaccgacacagguaggcgaggagagaauccuaaggugaucgaga
gaacucucguuaaggaacucggcaaaaugaccccguaacuucgggagaag
gggugcucuguuagggugcaagcccgagagagccgcagugaauaggccca
ggcgacuguuuaaacacaggucucugcgaagccguaaggcgaaguauagg
ggcugacgccucgcaacgaucugggcacugucucaacgagagacucggug
aaauuauaguaccugugaagaugcagguuacccgcgacaggacggaaaga
ccccguggagcuuuacugcagccugauauaacccgccgcccuuaucgggc
ggggagacagugucaggugggcaugguuccgcauggauccgucgcgggcg
caggaaauuugagaggagcuguccuuaguacgagaggaccgggauggacg
caccgcugguguaccaguuguucugccaagggcaucgcuggguagcuaug
ugcggacgggauaagugcugaaagcaucuaagcaugaagccccccucaag
augagauuucccauuccgcaaggaaguaagaucccugaaagaugaucagg
uugauaggucugagguggaaguguggcgacacauggagcugacagauacu
aaucgaucgaggacuuaac

<<<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<<.....
.<<<<<<.....((.>>>.....<<<<<<<..<<<)).....>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<<.....<.....
.>......>>>>>.>.........<<....>>...<<<<......<<...
..>>.....>>>>...<<<....<<<<<<........>>>>>>......<
<<<<<<.......<<<<.......<<<<<<<<<<.<<<.....<<<<...
...>>>>.((......<<<.....))>>>...>>>...>>>>>>>>>>>>
>>...>>>..>>>>.....<<<<<<<<....>>>>>>>>......<<<<<
..((((>>>>>..>>>......>>.>>>>>>>.>>...............
<<....>>....>>.........<<<<....>>>>...............
...>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>...
<.<........>.>.<<<<<<......<<<<<.<<<<<..<<<...<<<.
....>>>...>>>...<......>.....................>>>>>
.>>>>>....<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<
<<......>>>>>>.....>>>...<<<.<<<<<........>>>>>>>>
....>>>>>>>>>...<<<.....>>>......>>>>>>...>..>.>>.
.<<<<<<....<<<<<...>>>>><<<<<<<<<...<<<<<<<......>
>.>>>>>..>>>>>>>.>>..<<<<<<<..........>>>>>>>....<
<<......>>>...<<<<.<<<...<<<(((.....<<<<<<........
...<<..<<<<<<<<<..........>>>>>>>>>.>>...))).....>
>>>>>.>>>...>>>>>>><<<<<<..>>>>>>....>>>>>><<.<<..
.<.<<......<<<<<.<<....>>.>>>>>...>>.>...>>..>>...
..>>>>>><......<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...
<<<...<<<....>>>...>>>...>>....<<<<........>>>>.))
<<<<<.<<<<<.......<<...<<<<....<<<<..<<<..<<<.<.<<
<.<...[.[....>.>>>.<...<......<<.<.<<<<<<<.<<.....
>>>>>>>>>....>.>>......>....><..<<.......>>...>>.>
>>...>>>...>>>>.........>>>>..>>...>>>>>>>>>>>>>>.
.>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<.
...<<<<<<<..<<.........<.....<<<<<....<....>.....>
>>>><<<<<....<<<<....>>>>...>>>>>............<<<<<
<<<<..<<<....>>>..<<<<<<<.....<<<....>>>.......>>>
>>>>..<<...>>...>>.>>>>>>>..>..>>..>>>>>>>.>>>>.>.
....>.....<<<<<........>>>>>..<<<<<<<<.<<<........
.................<....<<........<<.<<<<<<.....>>>>
>>>>..........>>.....>..........)))).>>>>>>>>>>>..
..<<<<<<<...<<<<..<<<<<<<...............>>>>>>>.<<
<<<....<<<...<<<<<<<<<<<.].]>>>>>>..>>>>>...>>>..>
>>>>...<<<....<<<<<...........>>>>>....>>>.>>>>...
....>>>>>>>..<<<<....>>>>....<<<<<<<<.........>>>>
....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>
>...>>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pvk 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): K4 K5 M10 K15 G18 A26 K42 H44 S45 K46 G55 S66 M69 V78 R80 Y83 K90
• Binding residue (residue number reindexed from 1): K3 K4 M9 K14 G17 A25 K41 H43 S44 K45 G47 S58 M61 V70 R72 Y75 K79

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0009295 nucleoid
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6pvk, PDBe:6pvk, PDBj:6pvk
• PDBsum: 6pvk
• PubMed: 31665744
• UniProt: P0CI78|RL24_BACSU Large ribosomal subunit protein uL24 (Gene Name=rplX)