Structure of PDB 6gc6 Chain E Binding Site BS01

Receptor Information

>6gc6 Chain E (length=201) Species: 83333 (Escherichia coli K-12)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

Ligand information

>6gc6 Chain A (length=2092)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcaccaaacugcgaauaccggagaauguuaucacggg
agacacacggcgggugcuaacguccgucgugaagagggaaacaacccaga
ccgccagcuaaggucccaaagucaugguuaagugggaaacgcggaagaug
uaacggggcuaaaccaugcaccgaagcugcggcagcgacgcuuaugcguu
guuggguaggggagcguucuguaagccugcgaaggugugcugugaggcau
gcuggagguaucagaagugcgaaugcugacauaaguaacgauaaagcggg
ugaaaagcccgcucgccggaagaccaaggguuccuguccaacguuaaucg
gggcagggugagucgaccccuaaggcgaggccgaaaggcguagucgaugg
gaaacagguuaauauuccuguacuugguguuacugcgaaggggggacgga
gaaggcuauguuggccgggcgacgguugucccgguuuaagcguguaggcu
gguuuuccaggcaaauccggaaaaucaaggcugaggcgugaugacgaggc
acuacggugcugaagcaacaaaugcccugcuuccaggaaaagccucuaag
caucagguaacaucaaaucguaccccaaaccgacacagguggucagguag
agaauaccaaggcgcuugagagaacucgggugaaggaacuaggcaaaaug
gugccguaacuucgggagaaggcacgcugauauguaggugaggucccucg
cggauggagcugaaaucagucgaagauaccagcuggcugcaacuguuuau
uaaaaacacagcacugugcaaacacgaaaguggacguauacggugugacg
ccuggaauggcguaaugauggccaggcugucuccacccgagacucaguga
aauugaacucgcugugaagaugcaguguacccgcggcaagacggaaaucc
cuaucugccgugggcgcuggagaacugaggggggcugcuccuaguacgag
aggaccggaguggacgcaucacugguguucggguugucaugccaauggca
cugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagca
cgaaacuugccccgagaugaguucucccugacccuuuaaggguccugaag
gaacguugaagacgacgacguugauaggccggguguguaagcgcagcgau
gcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<....<.<<.<<<<<<<<<<<<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<......>..<<<<<<.....<<....
.>>....>>>>>>..<<<..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>.>..>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<......>>>>>..>>>......>>.>>>>>>>.>>.....
..........<<....>>....>>.........<<<<.....>>>>....
.........>....>>>>>>>>>>>.......<<<<..<<<<<......>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>..<<<<<<<...<<<
<<<<<<......<<.......>>.......>>>>>>.>>>...>>>>>>>
.....<<<<<<<<<<......>>>>>>>>>>....<<<......>>>...
<<<<.<<<...<<<(((.....<<<<<<...........<<>>.......
....))).....>>>>>>.>>>...>>>>>>><<<<<..<......>..>
>>>>....>>>>>><<<<<<<...<<<......<<<<<<<<....>>>>>
>>>...>>>..>>>>>.>>.....>>>>>><......<<.....<<<<<<
.......>>>>>><<<<....<<.<<.<<...<<<<<<...<<.....>>
.>>>>>>....((<<<.<<<...<<....<<<....>>>....>>...>>
>..<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....<<<
<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<<...<<<<
<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>>...>><..<<<
<<....>>>>>...>>>>>>...>>>...>>>>.........>>>>...>
>....>>>>>>>>>>>.>>>..>>.....<<......>>>>.>>.<<<<.
....>>>>..>>>>..<<<<....<<<<<<<<.<<...............
<<<<<.....<..>......>>>>><<<<<......<<<...<<<<....
.>>>>...>>>....>>>>>............<<<<<<<<<..<<<....
.....>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<
<<......>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>..
...>.....<<<<<........>>>>>..<<<<<<<<.<<<.<<.....>
>..>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.........
......>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>>>>
..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>>>>
>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>>.....<
<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<....>
>>>>...>>...>>>>>.>>>.....>>.....>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gc6 Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution.
• Resolution: 4.3 Å
• Binding residue (original residue number in PDB): H29 Q30 Y35 A36 G38 A39 R40 Q41 T43 R44 K47 T48 R49 V52 T53 G54 S55 K57 R67 A68 R69 G71 I77 W78 R79 S80 T84 F85 Q90 Q94 K95 N97 K98 K99 Y101 P129 K130 T131 K132 L159 N163 H165
• Binding residue (residue number reindexed from 1): H29 Q30 Y35 A36 G38 A39 R40 Q41 T43 R44 K47 T48 R49 V52 T53 G54 S55 K57 R67 A68 R69 G71 I77 W78 R79 S80 T84 F85 Q90 Q94 K95 N97 K98 K99 Y101 P129 K130 T131 K132 L159 N163 H165

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:6gc6, PDBe:6gc6, PDBj:6gc6
• PDBsum: 6gc6
• PubMed: 29883607
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)