Structure of PDB 4v5r Chain BG Binding Site BS02

Receptor Information

>4v5r Chain BG (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

Ligand information

>4v5r Chain BA (length=2901)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccgcaagggguuguggcgugccuauugaagcaugagccg
gcgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggg
aaaccgaguccgaacagggcgcaagcgggccgcacgcggcccgcaaaguc
cgcggccguggacccgaaaccgggcgagcuagcccuggccagggugaagc
uggggugagacccaguggaggcccgaaccggugggggaugcaaaccccuc
ggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcug
guucuccccgaaaugacuuuagggucagccucaggcgcugacuggggccu
guagagcacugauagggcuagggggcccaccagccuaccaaacccuguca
aacuccgaagggucccagguggagccugggagugagggcgcgagcgauaa
cguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccccca
agucugggcuaagugguaaaggauguggcgcggcgaagacagccaggagg
uuggcuuagaagcagccauccuuuaaagagugcguaauagcucacugguc
gaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcu
gcgggucugggggaugaccccaggcgguaggggagcguucccgaugccga
ugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaugccg
gcaugaguaacgauaaagagggugagaaucccucucgccguaagcccaag
gguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagguga
agccgaaaggcguagccgaagggcagccgguuaauauuccggcccuuccc
gcaggugcgauggggggacgcucuaggcuagggggaccggagccauggac
gagcccggccagaagcgcagggugggagguaggcaaauccgccucccaac
aagcucugcgugguggggaagcccguacgggugacaaccccccgaagcca
gggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaa
accgacacaggugggcgggugcaagagcacucaggcgcgcgggagaaccc
ucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggugc
ucccuggggugaugagccccggggagccgcagugaacaggcucuggcgac
uguuuaccaaaaacacagcucucugcgaacucguaagaggagguauaggg
agcgacgcuugcccggugccggaaggucaaggggaggggugcaagccccg
aaccgaagccccggugaacggcggccguaacuauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgacc
ggagcgcugucucggcgagggacccggugaaauugaacuggccgugaaga
ugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcag
ccugguguuggcucuuggucgcgccugcguaggauaggugggagccugug
aacccccgccuccgggugggggggaggcgccggugaaauaccacccuggc
gcggcugggggccuaacccucggauggggggacagcgcuuggcgggcagu
uugacuggggcggucgccuccuaaaagguaacggaggcgcccaaaggucc
ccucaggcgggacggaaauccgccggagagcgcaaggguagaagggggcc
ugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaa
ccgguggucccguguggaagggccaucgaucaacggauaaaaguuacccc
ggggauaacaggcugaucucccccgagcguccacagcggcggggagguuu
ggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaag
gguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgu
cgugagacaguucggucucuauccgccacgggcgcaggaggcuugagggg
ggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuccca
gcugucccuccaggggcauaagcuggguagccaugugcggaagggauaac
cgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacg
gcgucaagccgguaaggacccgggaagaccacccgguggaugggccgggg
guguaagcgccgcgaggcguugagccgaccggucccaaucguccgagguc
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v5r How Mutations in tRNA Distant from the Anticodon Affect the Fidelity of Decoding.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K36 V38 N40 G42 L43 T71 R72 A73 K75 N79 S124 R128 N130 N132 L133 G134 R136 G154 M155 D156 V160
• Binding residue (residue number reindexed from 1): K35 V37 N39 G41 L42 T70 R71 A72 K74 N78 S123 R127 N129 N131 L132 G133 R135 G153 M154 D155 V159

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA 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:4v5r, PDBe:4v5r, PDBj:4v5r
• PDBsum: 4v5r
• PubMed: 21378964
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)