Structure of PDB 6wnw Chain f Binding Site BS01

Receptor Information

>6wnw Chain f (length=176) Species: 562 (Escherichia coli)

SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLT
FGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGN
VINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAY
RRPEPYKGKGVRYADEVVRTKEAKKK

Ligand information

>6wnw Chain 4 (length=3031)

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
ucaacggauaaaagguacuccggggauaacaggcugauaccgcccaagag
uucauaucgacggcgguguuuggcaccucgaugucggcucaucacauccu
ggggcugaaguaggucccaaggguauggcuguucgccauuuaaaguggua
cgcgagcuggguuuagaacgucgugagacaguucggucccuaucugccgu
gggcgcuggagaacugaggggggcugcuccuaguacgagaggaccggagu
ggacgcaucacugguguucggguugucaugccaauggcacugcccgguag
cuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuugcc
ccgagaugaguucucccugacccuuuaaggguccugaaggaacguugaag
acgacgacguugauaggccggguguguaagcgcagcgaugcguugagcua
accgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wnw Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): S1 R2 V3 A62 Q63 G65 T66 A69 L70 F108 S109 K137 Q138 G141 Q142 R152 Y156 K157 K159 K171 K174
• Binding residue (residue number reindexed from 1): S1 R2 V3 A62 Q63 G65 T66 A69 L70 F108 S109 K137 Q138 G141 Q142 R152 Y156 K157 K159 K171 K174

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

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:6wnw, PDBe:6wnw, PDBj:6wnw
• PDBsum: 6wnw
• PubMed: 32518240
• UniProt: P0AG55|RL6_ECOLI Large ribosomal subunit protein uL6 (Gene Name=rplF)