Structure of PDB 6pvk Chain J Binding Site BS01

Receptor Information

>6pvk Chain J (length=141) Species: 1423 (Bacillus subtilis)

TPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGD
HVIIINAEKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLE
LAIKGMLPKGSLGRQMFKKLNVYRGSEHPHEAQKPEVYELR

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): T4 P5 G27 R28 S31 R38 K40 P47 H48 T66 K69 K73 H81 K86 A105 M109 S114 L115 R117 K121 A135 Q136
• Binding residue (residue number reindexed from 1): T1 P2 G24 R25 S28 R35 K37 P44 H45 T63 K66 K70 H78 K83 A102 M106 S111 L112 R114 K118 A132 Q133

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

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

External links

• PDB: RCSB:6pvk, PDBe:6pvk, PDBj:6pvk
• PDBsum: 6pvk
• PubMed: 31665744
• UniProt: P70974|RL13_BACSU Large ribosomal subunit protein uL13 (Gene Name=rplM)