Structure of PDB 6gc4 Chain E Binding Site BS01

Receptor Information

>6gc4 Chain E (length=201) Species: 83333 (Escherichia coli K-12)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

Ligand information

>6gc4 Chain A (length=2586)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcgucggcc
ugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcg
acgcuuaugcguuguuggguaggggagcguucuguaagccugcgaaggug
ugcugugaggcaugcuggagguaucagaagugcgaaugcugacauaagua
acgauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccugu
ccaacguuaaucggggcagggugagucgaccccuaaggcgaggccgaaag
gcguagucgaugggaaacagguuaauauuccuguacuugguguuacugcg
aaggggggacggagaaggcuauguuggccgggcgacgguugucccgguuu
aagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggc
gugaugacgaggcacuacggugcugaagcaacaaaugcccugcuuccagg
aaaagccucuaagcaucagguaacaucaaaucguaccccaaaccgacaca
gguggucagguagagaauaccaaggcgcuugagagaacucgggugaagga
acuaggcaaaauggugccguaacuucgggagaaggcacgcugauauguag
gugaggucccucgcggauggagcugaaaucagucgaagauaccagcuggc
ugcaacuguuuauuaaaaacacagcacugugcaaacacgaaaguggacgu
auacggugugacgccugcccgguguaaacggcggccguaacuauaacggu
ccuaagguagcgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauguguaggauaggugggaggcuuugaaguguggacgccagucugcaug
gagccgaccuugaaauaccacccuuuaauguuugauguucuaacguugac
ccguaauccggguugcggacagugucugguggguaguuugacuggggcgg
ucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugguc
ggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgu
gacggcgcgagcaggugcgaaagcaggucauagugauccggugguucuga
auggaagggccaucgcucaacggauaaaagguacuccggggucccuaucu
gccgugggcgcuggagaacugaggggggcugcuccuaguacgagaggacc
ggaguggacgcaucacugguguucggguugucaugccaauggcacugccc
gguagcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaac
uugccccgagaugaguucucccugacccuuuaaggguccugaaggaacgu
ugaagacgacgacguugauaggccggguguguaagcgcagcgaugcguug
agcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gc4 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): N24 L27 H29 Q30 V33 Y35 A36 G38 A39 R40 Q41 T43 R44 A45 T48 R49 V52 G54 S55 K57 K58 Q62 G66 R67 R69 G71 I77 W78 R79 S80 V83 F85 Q90 Q94 K95 N97 K98 K99 M100 Y101 K130 T131 K132 L159 A160 R162 N163 H165 T173
• Binding residue (residue number reindexed from 1): N24 L27 H29 Q30 V33 Y35 A36 G38 A39 R40 Q41 T43 R44 A45 T48 R49 V52 G54 S55 K57 K58 Q62 G66 R67 R69 G71 I77 W78 R79 S80 V83 F85 Q90 Q94 K95 N97 K98 K99 M100 Y101 K130 T131 K132 L159 A160 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:6gc4, PDBe:6gc4, PDBj:6gc4
• PDBsum: 6gc4
• PubMed: 29883607
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)