Structure of PDB 5vpp Chain R0 Binding Site BS01

Receptor Information

>5vpp Chain R0 (length=82) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRP

Ligand information

>5vpp Chain RA (length=2882)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccgcaagggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcaagcgcaaaguccgcggccguggacccgaaa
ccgggcgagcuagcccuggccagggugaagcuggggugagacccagugga
ggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagga
gugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuu
uagggucagccucaggcgcugacuggggccuguagagcacugauagggcu
agggggcccaccagccuaccaaacccugucaaacuccgaagggucccagg
uggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcgg
gaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaa
aggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccau
ccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacc
ccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagg
gcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaaga
gggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucg
ucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccga
agggcagccgguuaauauuccggcccuucccgcaggugcgauggggggac
gcucuaggcuagggggaccggagccauggacgagcccggccagaagcgca
gggugggagguaggcaaauccgccucccaacaagcucugcguggugggga
agcccguacgggugacaaccccccgaagccagggagccaagaaaagccuc
uaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcggg
ugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaa
guuggccccguaacuucgggagaaggggugcucccuggggugaugagccc
cggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagc
ucucugcgaacucguaagaggagguauagggagcgacgcuugcccggugc
cggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgag
ggacccggugaaauugaacuggccgugaagaugcggccuacccguggcag
gacgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggu
cgcgccugcguaggauaggugggagccugugaacccccgccuccgggugg
gggggaggcgccggugaaauaccacccuggcgcggcugggggccuaaccc
ucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccu
ccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaau
ccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaag
ccgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagcguccacagcggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccucccacggcgucaagccgguaaggac
ccgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcg
uugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vpp Mechanism of tRNA-mediated +1 ribosomal frameshifting.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): H3 K4 S9 T10 R11 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 A33 G34 N35 I36 R39 R41 G42 T43 G54 R55 D56 F57 T58 F60 L62 F69 R74 L75 R77
• Binding residue (residue number reindexed from 1): H2 K3 S8 T9 R10 N11 R13 D14 S15 Q16 A17 K18 R19 K23 R24 Y25 E26 Q28 A32 G33 N34 I35 R38 R40 G41 T42 G53 R54 D55 F56 T57 F59 L61 F68 R73 L74 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:5vpp, PDBe:5vpp, PDBj:5vpp
• PDBsum: 5vpp
• PubMed: 30262649
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)