Structure of PDB 5imr Chain a Binding Site BS01

Receptor Information

>5imr Chain a (length=272) Species: 300852 (Thermus thermophilus HB8)

KFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFR
GGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRY
IIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAK
LARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADHKNI
VLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWGWQT
KGLKTRKRRKPSSRFIIARRKK

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

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): R13 F15 M16 V18 K35 K39 R43 N45 Q46 G47 R48 T50 V51 R52 G56 G57 K59 L61 I64 D71 K72 I75 Y84 D85 P86 R88 D99 G100 E101 K102 E148 K151 K154 L155 A156 R157 A159 P178 R183 H186 N198 A199 K202 N203 L206 G207 K208 A209 G210 R211 R213 W214 L215 H220 V221 R222 G223 A224 M226 N227 V229 H231 H233 G234 G235 G236 E237 G238 R239 A240 P241 R242 R244 A247 P249 W250 W252 Q253 T254 K255 G256 L257 K258 R260 R262 R263 K264 R268
• Binding residue (residue number reindexed from 1): R9 F11 M12 V14 K31 K35 R39 N41 Q42 G43 R44 T46 V47 R48 G52 G53 K55 L57 I60 D67 K68 I71 Y80 D81 P82 R84 D95 G96 E97 K98 E144 K147 K150 L151 A152 R153 A155 P174 R179 H182 N194 A195 K198 N199 L202 G203 K204 A205 G206 R207 R209 W210 L211 H216 V217 R218 G219 A220 M222 N223 V225 H227 H229 G230 G231 G232 E233 G234 R235 A236 P237 R238 R240 A243 P245 W246 W248 Q249 T250 K251 G252 L253 K254 R256 R258 R259 K260 R264

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5imr, PDBe:5imr, PDBj:5imr
• PDBsum: 5imr
• PubMed: 27137929
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)