Structure of PDB 4v5m Chain BQ Binding Site BS01

Receptor Information

>4v5m Chain BQ (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Ligand information

>4v5m 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
agucugggcuaagugguaaaggauguggcgccgcgaagacagccaggagg
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: 4v5m Head Swivel on the Ribosome Facilitates Translocation by Means of Intra-Subunit tRNA Hybrid Sites.
• Resolution: 7.8 Å
• Binding residue (original residue number in PDB): R5 R6 K8 Y9 R10 K11 Q12 Q13 R14 G15 R16 K22 G23 G24 Y26 F29 W41 Q46 A49 R56 K63 R67 F69 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 L125 P126 K128 A140 Q141
• Binding residue (residue number reindexed from 1): R5 R6 K8 Y9 R10 K11 Q12 Q13 R14 G15 R16 K22 G23 G24 Y26 F29 W41 Q46 A49 R56 K63 R67 F69 K76 K77 E80 R82 M83 G84 K85 G86 K87 R101 R119 H123 K124 L125 P126 K128 A140 Q141

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:4v5m, PDBe:4v5m, PDBj:4v5m
• PDBsum: 4v5m
• PubMed: 21124459
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)