Structure of PDB 6enf Chain 3 Binding Site BS01

Receptor Information

>6enf Chain 3 (length=64) Species: 562 (Escherichia coli)

PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVS
KGDLGLVIACLPYA

Ligand information

>6enf Chain A (length=2807)

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
acggaaagaccccguaaaccuuuacuauagcuugacacugaaugauguuc
uaacguugacccguaauccggguugcggacagugucugguggguaguuug
acuggggcggucuccuccuaaagaguaacggaggagcacgaagguuggcu
aauccuggucggacaucaggagguuagugcaauggcauaagccagcuuga
cugcgagcgugacggcgcgagcaggugcgaaagcaggucauagugauccg
gugguucugaauggaagggccaucgcucaacggauaaaagguacuccggg
gauaacaggcugauaccgcccaagaguucauaucgacggcgguguuuggc
accucgaugucggcucaucacauccuggggcugaaguaggucccaagggu
auggcuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgu
gagacaguucggucccuaucugccgugggcgcuggagaacugaggggggc
ugcuccuaguacgagaggaccggaguggacgcaucacugguguucggguu
gucaugccaauggcacugcccgguagcuaaaugcggaagagauaagugcu
gaaagcaucuaagcacgaaacuugccccgagaugaguucucccugacccu
uuaaggguccugaaggaacguugaagacgacgacguugauaggccgggug
uguaagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggc
uuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6enf Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): P1 K2 I3 K4 T5 R7 K11 R12 T16 G17 K18 K22 H25 A26 N27 R29 H30 I31 L32 T33 K34 K35 T37 K38 R39 K40 R41 H42 L43 R44 K46 K51 G52 D53 Y63
• Binding residue (residue number reindexed from 1): P1 K2 I3 K4 T5 R7 K11 R12 T16 G17 K18 K22 H25 A26 N27 R29 H30 I31 L32 T33 K34 K35 T37 K38 R39 K40 R41 H42 L43 R44 K46 K51 G52 D53 Y63

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6enf, PDBe:6enf, PDBj:6enf
• PDBsum: 6enf
• PubMed: 29100052
• UniProt: P0A7Q1|RL35_ECOLI Large ribosomal subunit protein bL35 (Gene Name=rpmI)