Structure of PDB 4v8q Chain A0 Binding Site BS01

Receptor Information

>4v8q Chain A0 (length=84) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA

Ligand information

>4v8q Chain AA (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
aaccgaagccccggugaacggcggccguaaauauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgacc
ggagcgcugucucggcgagggacccggugaaauugaacuggccgugaaga
ugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcag
ccugguguuggcucuuggucgcgccugcguaggauaggugggagccugug
aacccccgccuccgggugggggggaggcgccggugaaauaccacccuggc
gcggcugggggccuaacccucggauggggggacagcgcuuggcgggcagu
uugacuggggcggucgccuccuaaaagguaacggaggcgcccaaaggucc
ccucaggcgggacggaaauccgccggagagcgcaaggguagaagggggcc
ugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaa
ccgguggucccguguggaagggccaucgaucaacggauaaaaguuacccc
ggggauaacaggcugaucucccccgagcguccacagcggcggggagguuu
ggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaag
gguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgu
cgugagacaguucggucucuauccgccacgggcgcaggaggcuugagggg
ggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuccca
gcugucccuccaggggcauaagcuggguagccaugugcggaagggauaac
cgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacg
gcgucaagccgguaaggacccgggaagaccacccgguggaugggccgggg
guguaagcgccgcgaggcguugagccgaccggucccaaucguccgagguc
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8q Decoding in the absence of a codon by tmRNA and SmpB in the ribosome.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): A2 H3 K4 S9 N12 R14 D15 S16 Q17 A18 K19 R20 K24 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 G54 R55 D56 F57 F60 F69 R77
• Binding residue (residue number reindexed from 1): A1 H2 K3 S8 N11 R13 D14 S15 Q16 A17 K18 R19 K23 Y25 E26 Q28 R31 A32 G33 N34 I35 R38 R40 G41 T42 G53 R54 D55 F56 F59 F68 R76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v8q, PDBe:4v8q, PDBj:4v8q
• PDBsum: 4v8q
• PubMed: 22422985
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)