Structure of PDB 6pvk Chain S Binding Site BS01

Receptor Information

>6pvk Chain S (length=101) Species: 1423 (Bacillus subtilis)

QAKAVARTVRIAPRKARLVMDLIRGKQVGEAVSILNLTPRAASPIIEKVL
KSAIANAEHNYEMDANNLVISQAFVDEGPTLKRFSQINKRTSHITIVVSE
K

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): V6 R8 R11 R15 K16 R18 R25 R41 A42 K49 N57 N61 S94 I96 N97
• Binding residue (residue number reindexed from 1): V5 R7 R10 R14 K15 R17 R24 R40 A41 K48 N56 N60 S85 I87 N88

Gene Ontology

Molecular Function

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

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:6pvk, PDBe:6pvk, PDBj:6pvk
• PDBsum: 6pvk
• PubMed: 31665744
• UniProt: P42060|RL22_BACSU Large ribosomal subunit protein uL22 (Gene Name=rplV)