Structure of PDB 6wnv Chain o Binding Site BS01

Receptor Information

>6wnv Chain o (length=116) Species: 562 (Escherichia coli)

DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAA
STVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHG
RVQALADAAREAGLQF

Ligand information

>6wnv Chain 4 (length=3025)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggcugcuccccaugcgagaguaggga
acugccaggcauucggugccuggcggccguagcgcgguggucccaccuga
ccccaugccgaacucagaagugaaacgccguagcgccgaugguagugugg
gguaaaacgaugugggaaggcccagacagccaggauguuggcuuagaagc
agccaucauuuaaagaaagcguaauagcucacuggucgagucggccugcg
cggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgc
uuaugcguuguuggguaggggagcguucuguaagccugcgaaggugugcu
gugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaacga
uaaagcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaa
cguuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggcgu
agucgaugggaaacagguuaauauuccuguacuugguguuacugcgaagg
ggggacggagaaggcuauguuggccgggcgacgguugucccgguuuaagc
guguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcguga
ugacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaaaa
gccucuaagcaucagguaacaucaaaucguaccccaaaccgacacaggug
gucagguagagaauaccaaggcgcuugagagaacucgggugaaggaacua
ggcaaaauggugccguaacuucgggagaaggcacgcugauauguagguga
ggucccucgcggauggagcugaaaucagucgaagauaccagcuggcugca
acuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguauac
ggugugacgccugcccggugccggaagguuaauugaugggguuagcgcaa
gcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaacgg
uccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaug
gcguaaugauggccaggcugucuccacccgagacucagugaaauugaacu
cgcugugaagaugcaguguacccgcggcaagacggaaagaccccgugaac
cuuuacuauagcuugacacugaacauugagccuugauguguaggauaggu
gggaggcuuugaaguguggacgccagucugcauggagccgaccuugaaau
accacccuuuaauguuugauguucuaacguugacccguaauccggguugc
ggacagugucugguggguaguuugacuggggcggucuccuccuaaagagu
aacggaggagcacgaagguuggcuaauccuggucggacaucaggagguua
gugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcaggu
gcgaaagcaggucauagugauccggugguucugaauggaagggccaucgc
ucaacggauaaaagguacuccggggaucugauaccgcccaagaguucaua
ucgacggcgguguuuggcaccucgaugucggcucaucacauccuggggcu
gaaguaggucccaaggguauggcuguucgccauuuaaagugguacgcgag
cuggguuuagaacgucgugagacaguucggucccuaucugccgugggcgc
uggagaacugaggggggcugcuccuaguacgagaggaccggaguggacgc
aucacugguguucggguugucaugccaauggcacugcccgguagcuaaau
gcggaagagauaagugcugaaagcaucuaagcacgaaacuugccccgaga
ugaguucucccugacccuuuaaggguccugaaggaacguugaagacgacg
acguugauaggccggguguguaagcgcagcgaugcguugagcuaaccggu
acuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wnv Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): K3 R9 R10 T12 R13 R15 R25 H29 R30 T31 P32 R33 H34 Y36 Q38 G44 S45 V47 V54 K63 Y64 N67 K68 S91 F92 R94 Q98 Y99 H100 G101 R102 R111
• Binding residue (residue number reindexed from 1): K2 R8 R9 T11 R12 R14 R24 H28 R29 T30 P31 R32 H33 Y35 Q37 G43 S44 V46 V53 K62 Y63 N66 K67 S90 F91 R93 Q97 Y98 H99 G100 R101 R110

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6wnv, PDBe:6wnv, PDBj:6wnv
• PDBsum: 6wnv
• PubMed: 32518240
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)