Structure of PDB 8e3l Chain M Binding Site BS01

Receptor Information

>8e3l Chain M (length=201) Species: 562 (Escherichia coli)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

Ligand information

>8e3l Chain I (length=2897)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auguguaggauaggugggaggcuuugaaguguggacgccagucugcaugg
agccgaccuugaaauaccacccuuuaauguuugauguucuaacguugacc
cguaauccggguugcggacagugucugguggguaguuugacuggggcggu
cuccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucg
gacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgug
acggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaa
uggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcu
gauaccgcccaagaguucauaucgacggcgguguuuggcaccucgauguc
ggcucaucacauccuggggcugaaguaggucccaaggguauggcuguucg
ccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucg
gucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagua
cgagaggaccggaguggacgcaucacugguguucggguugucaugccaau
ggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucua
agcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccu
gaaggaacguugaagacgacgacguugauaggccggguguguaagcgcag
cgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e3l Solithromycin siderophore conjugates
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): H29 Q30 Y35 R40 Q41 T43 R44 K47 R49 T53 S55 K57 K58 K63 T65 R67 R69 G71 I77 W78 R79 S80 T84 F85 K95 K98 K99 R102 K130 T131 K132 R162 N163 H165
• Binding residue (residue number reindexed from 1): H29 Q30 Y35 R40 Q41 T43 R44 K47 R49 T53 S55 K57 K58 K63 T65 R67 R69 G71 I77 W78 R79 S80 T84 F85 K95 K98 K99 R102 K130 T131 K132 R162 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:8e3l, PDBe:8e3l, PDBj:8e3l
• PDBsum: 8e3l
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)