Structure of PDB 5imr Chain m Binding Site BS01

Receptor Information

>5imr Chain m (length=117) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQG

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

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

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): P2 R3 K5 T6 V8 V9 R10 R11 R12 K13 H14 K15 K19 K22 G23 W25 L27 R28 K30 F32 R33 K34 E37 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 W61 N75 S77 H81 K84 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 K4 T5 V7 V8 R9 R10 R11 K12 H13 K14 K18 K21 G22 W24 L26 R27 K29 F31 R32 K33 E36 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 W60 N74 S76 H80 K83 R91 K92

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5imr, PDBe:5imr, PDBj:5imr
• PDBsum: 5imr
• PubMed: 27137929
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)