Structure of PDB 6enj Chain X Binding Site BS01

Receptor Information

>6enj Chain X (length=77) Species: 562 (Escherichia coli)

SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRV
SAKGMRVIDKKGIDTVLAELRARGEKY

Ligand information

>6enj Chain A (length=2871)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacgacuuaccaaccc
gaugcaaacugcgaauaccggagaauguuaucacgggagacacacggcgg
gugcuaacguccgucgugaagagggaaacaacccagaccgccagcuaagg
ucccaaagucaugguuaagugggaaacgaugugggaaggcccagacagcc
aggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagcuca
cuggucgagucggccugcgcggaagauguaacggggcuaaaccaugcacc
gaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguucugu
aagccugcgaaggugugcugugaggcaugcuggagguaucagaagugcga
augcugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaag
accaaggguuccuguccaacguuaaucggggcagggugagucgaccccua
aggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccugua
cuugguguuacugcgaaggggggacggagaaggcuauguuggccgggcga
cgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaa
aaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaa
ugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucgua
ccccaaaccgacacagguggucagguagagaauaccaaggcgcuugagag
aacucgggugaaggaacuaggcaaaauggugccguaacuucgggagaagg
cacgcugauauguaggugaggucccucgcggauggagcugaaaucagucg
aagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaa
cacgaaaguggacguauacggugugacgccugcccggugccgggagguua
auugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacg
gcggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaa
guuccgaccugcacgaauggcguaaugauggccaggcugucuccacccga
gacucagugaaauugaacucgcugugaagaugcaguguacccgcggcaag
acggaaagaccccguaaaccuuuacuauagcuugacacugaacauugagc
uuugauguguaggauaggugggaggagccgaccuugaaauaccacccuuu
aauguuugauguucuaacguugacccguaauccggguugcggacaguguc
ugguggguaguuugacuggggcggucuccuccuaaagaguaacggaggag
cacgaagguuggcuaauccuggucggacaucaggagguuagugcaauggc
auaagccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcag
gucauagugauccggugguucugaauggaagggccaucgcucaacggaua
aaagguacuccggggauaacaggcugauaccgcccaagaguucauaucga
cggcgguguuuggcaccucgaugucggcucaucacauccuggggcugaag
uaggucccaaggguauggcuguucgccauuuaaagugguacgcgagcugg
guuuagaacgucgugagacaguucggucccuaucugccgugggcgcugga
gaacugaggggggcugcuccuaguacgagaggaccggaguggacgcauca
cugguguucggguugucaugccaauggcacugcccgguagcuaaaugcgg
aagagauaagugcugaaagcaucuaagcacgaaacuugccccgagaugag
uucucccugacccuuuaaggguccugaaggaacguugaagacgacgacgu
ugauaggccggguguguaagcgcagcgaugcguugagcuaaccgguacua
augaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6enj Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): S1 R2 K9 R10 T13 N15 R17 S18 A20 L21 N22 K25 R26 R27 L29 P30 N31 H33 H35 R36 R49 A52 M55 R56 K60 K76
• Binding residue (residue number reindexed from 1): S1 R2 K9 R10 T13 N15 R17 S18 A20 L21 N22 K25 R26 R27 L29 P30 N31 H33 H35 R36 R49 A52 M55 R56 K60 K76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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:6enj, PDBe:6enj, PDBj:6enj
• PDBsum: 6enj
• PubMed: 29100052
• UniProt: P0A7M2|RL28_ECOLI Large ribosomal subunit protein bL28 (Gene Name=rpmB)