Structure of PDB 4v5e Chain BQ Binding Site BS01

Receptor Information

>4v5e Chain BQ (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Ligand information

>4v5e Chain BA (length=2886)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcaagggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgggccgcacgcggcccgcaaaguccgcggc
cguggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggu
gagacccaguggaggcccgaaccggugggggaugcaaaccccucggauga
gcuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucuc
cccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagag
cacugauagggcuagggggcccaccagccuaccaaacccugucaaacucc
gaagggucccagguggagccugggagugagggcgcgagcgauaacguccg
cguccgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucug
ggcuaagugguaaaggauguggcgcggcgaagacagccaggagguuggcu
uagaagcagccauccuuuaaagagugcguaauagcucacuggucgagucg
cgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggu
cugggggaugaccccaggcgguaggggagcguucccgaugccgaugaagg
ccgacccgcgagggcggcuggagguaagggaagugcgaaugccggcauga
guaacgauaaagagggugagaaucccucucgccguaagcccaaggguucc
uacgcaauggucgucagcguaggguuaggcgggaccuaaggugaagccga
aaggcguagccgaagggcagccgguuaauauuccggcccuucccgcaggu
gcgauggggggacgcucuaggcuagggggaccggagccauggacgagccc
ggccagaagcgcagggugggagguaggcaaauccgccucccaacaagcuc
ugcgugguggggaagcccgcaaccccccgaagccagggagccaagaaaag
ccucuaagcacaaccugcgggaacccguaccgcaaaccgacacagguggg
cgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucu
gcaaguuggccccguaacuucgggagaaggggugcucccuggggugauga
gccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaaca
cagcucucugcgaacucguaagaggagguauagggagcgacgcuugcccg
gugccggaaggucaaggggaggggugcaagccccgaaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucgg
cgagggacccggugaaauugaacuggccgugaagaugcggccuacccgug
gcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcucu
uggucgcgccugcguaggauaggugggagccugugaacccccgccuccgg
gugggggggaggcgccggugaaauaccacccuggcgcggcugggggccua
acccucggauggggggacagcgcuuggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgg
aaauccgccggagagcgcaaggguagaagggggccugacugcgaggccug
caagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugu
ggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcug
aucucccccgagcguccacagcggcggggagguuuggcaccucgaugucg
gcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgc
ccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgg
ucucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguac
gagaggaccggaagggacgcaccucugguuucccagcugucccuccaggg
gcauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucua
agcgggaagcccgccccaagaugaggccucccacggcgucaagccgguaa
ggacccgggaagaccacccgguggaugggccggggguguaagcgccgcga
ggcguugagccgaccggucccaaucguccgaggucu

.<.......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
..>>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>....
.....<<....>>...<<<<<.....<<.....>>....>>>>>...<<<
....<<<<<<<<.....>>>>>>>>.....<<<<<<<<<<.<<...<<<<
<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))>>>
...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<<<.
......>>>>>>>>>......<<<<<..((((>>>>>..>>>......>>
.>>>>>>.>>...............<<....>>....>>.........<<
<<....>>>>..................>>>>>>>>>>>.......<<<<
<<<<<<<....>>>>>>>>>>>...<............>.<<<<<<....
<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>.
.<<<<.....>>>>....<<<<<<<<....>>>>>>>>...>>>>>>>>>
>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<..
....>>>>>>.....>>>...<<<..<<<<........>>>>.>>>....
>>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<
<<<....<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<
...<<<<<<<<.<.<<<<<<......>>>>.>>>..>>>>>>>>..>>.>
...>>>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>
>>>>>.....<<<......>>>...<<<<.<<<...<<<(((.....<<<
<<<...........<<..<<<<<<<<<........<<<<<.<<...<<<<
.......>>>>...>>.........<<......>>...>>>>>....>>>
>>>>>>.>>..........)))......>>>>>>.>>>...>>>>>>><<
<<<<<.......>>>>>>>....>>>>>>..<<<<<...<<<......<<
<<<.<<<....>>>>>>>>...>>>..>>>>>........>>>>>><...
...<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<
<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<..
..>>>...>>>...>>...<<<<<........>>>>>))<<<<<<<<<<<
<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>
>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>
>>>>>..>>><...........>>>>>>...>>>..>>>>>.........
>>>>...>>...>>>>>>>>>>>>>>>..>>.....<<......>>>>>>
>.<<<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<.......
..<.....<<<<<.....<..>......>>>>><<<<<<<<<<<<.....
>>>>>>>>>>>>............<<<<<<<<<..<<<.........>>>
..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..
<<<<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>>>>>>
..>>>>><<<<<<.......>>>>>>........<...........<<<<
<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>
>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<
<<.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<
<<<<<<<<<<...........<<<<<..<<<......<<<<<<<<....>
>>>>>>>...>>>............>>>>>..>>>>>>>>>>>>>>>>..
.<<<<<....>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>>
<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<....
...>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<...
...>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<<..))
))..>>>>>>>>>.............>>>>..>>>>>>.......<<<<.
..<<<<<<...<<.......>>...>>>>>>....>>>.>.......<<<
<<..<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>
>>>.....>>>>>......>>>.>>....<<<<<<<....>>>.>>>>..
......>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<......
.........>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>
>>>...>>>>>...>>>>.>>>>>...<<<....<<<<<...........
>>>>>....>>>.>>>>.......>>>>>>>...<.........>.....
<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....
>>>>>...>>>..>>>>>.>>>...>>>>.....>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v5e Insights Into Translational Termination from the Structure of Rf2 Bound to the Ribosome.
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): P4 R5 R6 K8 Y9 R10 K11 Q12 Q13 R14 G15 R16 K22 G24 Y26 W41 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 G88 R101 R119 I120 H123 K124 P126 K128 E139
• Binding residue (residue number reindexed from 1): P4 R5 R6 K8 Y9 R10 K11 Q12 Q13 R14 G15 R16 K22 G24 Y26 W41 Q46 A49 R56 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 K85 G86 K87 G88 R101 R119 I120 H123 K124 P126 K128 E139

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v5e, PDBe:4v5e, PDBj:4v5e
• PDBsum: 4v5e
• PubMed: 18988853
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)