Structure of PDB 6gxn Chain E Binding Site BS01

Receptor Information

>6gxn Chain E (length=201) Species: 562 (Escherichia coli)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

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): N24 H29 Q30 Y35 A36 G38 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 T53 G54 S55 K57 K58 Q62 K63 G64 T65 G66 R67 A68 R69 G71 S75 W78 R79 V83 F85 Q90 Q94 K95 N97 K98 K99 Y101 P129 K130 T131 K132 L159 R162 N163 H165 T173
• Binding residue (residue number reindexed from 1): N24 H29 Q30 Y35 A36 G38 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 T53 G54 S55 K57 K58 Q62 K63 G64 T65 G66 R67 A68 R69 G71 S75 W78 R79 V83 F85 Q90 Q94 K95 N97 K98 K99 Y101 P129 K130 T131 K132 L159 R162 N163 H165 T173

Gene Ontology

Molecular Function

• GO:0001070 RNA-binding transcription regulator activity
• GO:0003677 DNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0030371 translation repressor activity
• GO:0048027 mRNA 5'-UTR binding
• GO:0060698 endoribonuclease inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006353 DNA-templated transcription termination
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0031555 transcriptional attenuation
• GO:0042255 ribosome assembly
• GO:0045892 negative regulation of DNA-templated transcription
• GO:0046677 response to antibiotic
• GO:2000766 negative regulation of cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6gxn, PDBe:6gxn, PDBj:6gxn
• PDBsum: 6gxn
• PubMed: 30076302
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)