Structure of PDB 5imr Chain 3 Binding Site BS01

Receptor Information

>5imr Chain 3 (length=134) Species: 300852 (Thermus thermophilus HB8)

VVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIV
PVEITIYADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQ
VLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVE

Ligand information

>5imr Chain D (length=2889)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuugcgcggggggaaccuggggaacugaaacaucucaguaccca
gaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaagggg
accagccuaaaccguccggcuuguccgggcggggucguggggcccucgga
caccgaauccccagccuagccgaagcuguugggaagcagcgccagagagg
gugaaagccccguaggcgaaagguggggggauaggugaggguacccgagu
accccgugguucguggagccaugggggaaucugggcggaccaccgccuaa
ggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagg
ugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuu
acaagcagucacggccccgcaagggguuguggcgugccuauugaagcaug
agccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcg
uagggaaaccgaguccgaacagggcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcc
auccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaugcggggcuuaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
aggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
gggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaac
ccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgc
cuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaa
auccgccggagagcgcaaggguagaagggggccugacugcgaggccugca
agccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugg
aagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugau
cucccccgagcguccacagcggcggggagguuuggcaccucgaugucggc
ucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccc
auuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgguc
ucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacga
gaggaccggaagggacgcaccucugguuucccagcugucccuccaggggc
auaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaag
cgggaagcccgccccaagaugaggccucccacggcgucaagccgguaagg
acccgggaagaccacccgguggaugggccggggguguaagcgccgcgagg
cguugagccgaccggucccaaucguccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5imr Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome
• Resolution: 5.7 Å
• Binding residue (original residue number in PDB): K9 L10 Q11 P13 P25 A26 P73 A74 S75 I78 K86 G87 A88 K90 P91 G92 L115 R125 M126 I127 A128 G129 S130 A131 R132 S133 E137
• Binding residue (residue number reindexed from 1): K6 L7 Q8 P10 P22 A23 P70 A71 S72 I75 K83 G84 A85 K87 P88 G89 L112 R122 M123 I124 A125 G126 S127 A128 R129 S130 E134

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5imr, PDBe:5imr, PDBj:5imr
• PDBsum: 5imr
• PubMed: 27137929
• UniProt: Q5SLP6|RL11_THET8 Large ribosomal subunit protein uL11 (Gene Name=rplK)