Structure of PDB 5imq Chain a Binding Site BS02

Receptor Information

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

KFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFR
GGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRY
IIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAK
LARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADHKNI
VLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWGWQT
KGLKTRKRRKPSSRFIIARRKK

Ligand information

>5imq 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: 5imq Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): R13 F15 M16 T17 V18 F21 I24 K26 K35 K38 K39 G42 R43 Q46 R48 I49 T50 V51 R52 F53 K59 L61 Y62 R63 W70 I75 Y84 D85 P86 R88 D99 G100 E101 K150 K151 K154 A156 R157 A158 A159 T161 Y172 L177 P178 S179 H186 A199 K202 V205 L206 G207 K208 A209 G210 R211 R213 W214 L215 R217 R218 H220 V221 R222 G223 A224 A225 M226 N227 V229 D230 H231 G235 G236 E237 G238 R239 A240 P241 R242 R244 P245 P249 W250 Q253 T254 K255 L257 K258 R260 R262 R263 R268
• Binding residue (residue number reindexed from 1): R9 F11 M12 T13 V14 F17 I20 K22 K31 K34 K35 G38 R39 Q42 R44 I45 T46 V47 R48 F49 K55 L57 Y58 R59 W66 I71 Y80 D81 P82 R84 D95 G96 E97 K146 K147 K150 A152 R153 A154 A155 T157 Y168 L173 P174 S175 H182 A195 K198 V201 L202 G203 K204 A205 G206 R207 R209 W210 L211 R213 R214 H216 V217 R218 G219 A220 A221 M222 N223 V225 D226 H227 G231 G232 E233 G234 R235 A236 P237 R238 R240 P241 P245 W246 Q249 T250 K251 L253 K254 R256 R258 R259 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:5imq, PDBe:5imq, PDBj:5imq
• PDBsum: 5imq
• PubMed: 27137929
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)