Structure of PDB 6gxn Chain F Binding Site BS01

Receptor Information

>6gxn Chain F (length=177) Species: 562 (Escherichia coli)

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFR

Ligand information

>6gxn Chain A (length=2895)

guuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgaug
aaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguua
uaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuauc
auuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacauc
uaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcga
gcgaacggggagcagcccagagccugaaucaguguguguguuaguggaag
cgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaugc
acaugcugugagcucgaugaguagggcgggacacgugguauccugucuga
auauggggggaccauccuccaaggcuaaauacuccugacugaccgauagu
gaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggaguga
aaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggcg
ugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagc
aagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcg
uuaaguugcaggguauagacccgaaacccggugaucuagccaugggcagg
uugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaaa
aauuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggag
auagcugguucuccccgaaagcuauuuagguagcgccucgugaauucauc
uccggggguagagcacuguuucggcaaggggguacuuaccaacccgaugc
aaacugcgaauaccggagaauguuaucacgggagacacacggcgggugcu
aacguccgucgugaagagggaaacaacccagaccgccagcuaagguccca
aagucaugguuaagugggaaacgaugugggaaggcccagacagccaggau
guuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacuggu
cgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaagc
ugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagcc
ugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcu
gacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaa
ggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggcg
aggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuugg
uguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgguu
gucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauca
aggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugccc
ugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccca
aaccgacacagguggucagguagagaauaccaaggcgcuugagagaacuc
gggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgc
ugauauguaggugaggucccucgcggauggagcugaaaucagucgaagau
accagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacga
aaguggacguauacggugugacgccugcccggugccgggagguuaauuga
ugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaauggcguaaugauggccaggcugucuccacccgagacuc
agugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgga
aagaccccgugaaccuuuacuauagcuugacacugaacauugagccuuga
uguguaggauaggugggaggcuuugaaguguggacgccagucugcaugga
gccgaccuugaaauaccacccuuuaauguuugauguucuaacguugaccc
guaauccggguugcggacagugucugguggguaguuugacuggggcgguc
uccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucgg
acaucaggagguuagugcaauggcauaagccagcuugacugcgagcguga
cggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaau
ggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcug
auaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugucg
gcucaucacauccuggggcugaaguaggucccaaggguauggcuguucgc
cauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucgg
ucccuaucugccgugggcgcuggagaacugaggggggcugcuccuaguac
gagaggaccggaguggacgcaucacugguguucggguugucaugccaaug
gcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaa
gcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccug
aaggaacguugaagacgacgacguugauaggccggguguguaagcgcagc
gaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<....
..<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..].>>>....
..>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<
<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>
......>>>>>.>.........<......>..<<<<<<.....<<.....
>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...<
<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>>
>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>..
....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]]......
.........<<....>>....]].........<<<<.....>>>>.....
........}....>>>>>>>>>>>.......<<<<..<<<<<<<..>>>>
>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<<
..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>.
....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<
<<...<<<<<<......>>>>>>...>.>>>...<<<.<<<<<.......
.>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>..
.>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<<
<<<<<.....<<<...<<<.<<<<...<<<.....>..>>...>>>>.>>
>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<...
...>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.
....<<<<<<...........<<..<<<<<..<<........<<<<<.<.
....<<.........>>.....>........<<<......>>>..>>>>>
....>>..>>>>>.>>...........))).....>>>>>>.>>>...>>
>>>>><<<<<..<......>..>>>>>....>>>>>><.<<<<<...<<<
......<<<<<<<<....>>>>>>>>...>>>..>>>>>..>.....>>>
>>><......<<.....<<<<<<.......>>>>>><<<<....<<<<<.
<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<.
..<<<....>>>...>>>...>>>..<<<<<........>>>>>))<<<<
<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((.
..>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>.
.>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>.
..>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>...
..<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<
<<<<<.<<...............<<<<<....<<..>>.....>>>>><<
<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>>.......
.....<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<..
..>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<.......
.<<<<<<.<<....>>..>>>>>>........>>>>>>>>..>>>>><<<
<<<.......>>>>>>........<...........<<<<<<.....>>>
>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>
>>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[.
.....<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<<
...........<<<<<..<<<......<<<<<<<<....>>>>>>>>...
>>>............>>>>>..>>>>.>>>>>>>>>>>...<<<.<<<<<
<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>>
<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<....
...>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<<..
..>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.((..>>
>>..))>>>>>>>.............>>>>..]]>>>>.......<<<<.
..<<<<<<...<<.......>>...>>>>>>....>>>.>.......<<<
<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>
>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>..
..]]..)))>>>>>>>>....<<<<<<<...<<<<...<<<<<<......
.........>>>>>>..<<<<<...<<<<...<<<<<<<<<<<))).>>>
>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>
>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>>...
..<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<..
..>>>>>...>>...>>>>>.>>>.....>>.....>>>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gxn Visualization of translation termination intermediates trapped by the Apidaecin 137 peptide during RF3-mediated recycling of RF1.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): K32 N36 G38 V39 G40 E41 A69 R70 K71 F76 I78 K87 D122 N126 V148 R149 G150
• Binding residue (residue number reindexed from 1): K32 N36 G38 V39 G40 E41 A69 R70 K71 F76 I78 K87 D122 N126 V148 R149 G150

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:6gxn, PDBe:6gxn, PDBj:6gxn
• PDBsum: 6gxn
• PubMed: 30076302
• UniProt: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)