Structure of PDB 6nta Chain Y8 Binding Site BS01

Receptor Information

>6nta Chain Y8 (length=64) Species: 300852 (Thermus thermophilus HB8)

PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLA
KPEAERIKLLLPYE

Ligand information

>6nta Chain YA (length=2883)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucguggggcccucggacaccgaa
uccccagccuagccgaagcuguugggaagcagcgccagagagggugaaag
ccccguaggcgaaagguggggggauaggugaggguacccgaguaccccgu
gguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaag
uacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaag
aaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagca
gucacggccccgcaagggguuguggcgugccuauugaagcaugagccggc
gacucacggucgugggcgagcuuaagccguugaggcggaggcguagggaa
accgaguccgaacagggcgcaagcgcaaaguccgcggccguggacccgaa
accgggcgagcuagcccuggccagggugaagcuggggugagacccagugg
aggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagg
agugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacu
uuagggucagccucaggcgcugacuggggccuguagagcacugauagggc
uagggggcccaccagccuaccaaacccugucaaacuccgaagggucccag
guggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcg
ggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggua
aaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcca
uccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaa
aaugaucggggcuuaagcccagcgccgaagcugcgggucugggggaugac
cccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgag
ggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaag
agggugagaaucccucucgccguaagcccaaggguuccuacgcaaugguc
gucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccg
aagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggga
cgcucuaggcuagggggaccggagccauggacgagcccggccagaagcgc
agggugggagguaggcaaauccgccucccaacaagcucugcguggugggg
aagcccguacgggugacaaccccccgaagccagggagccaagaaaagccu
cuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgg
gugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugca
aguuggccccguaacuucgggagaaggggugcucccuggggugaugagcc
ccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacag
cucucugcgaacucguaagaggagguauagggagcgacgcuugcccggug
ccggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaa
cggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggu
aaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcga
gggacccggugaaauugaacuggccgugaagaugcggccuacccguggca
ggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuugg
ucgcgccugcguaggauaggugggagccugugaacccccgccuccgggug
ggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaacc
cucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgcc
uccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaa
uccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaa
gccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugga
agggccaucgaucaacggauaaaaguuaccccggggauaacaggcugauc
ucccccgagcguccacagcggcggggagguuuggcaccucgaugucggcu
cgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccca
uuaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucu
cuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgag
aggaccggaagggacgcaccucugguuucccagcugucccuccaggggca
uaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagc
gggaagcccgccccaagaugaggccucccacggcgucaagccgguaagga
cccgggaagaccacccgguggaugggccggggguguaagcgccgcgaggc
guugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6nta Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 K3 M4 K5 T6 H7 K8 K12 R13 K15 T17 A18 S19 K21 K26 T27 G28 K29 R30 H31 L32 N33 W34 Q35 G38 K39 R42 Q43 K44 R46 K47 L50 A51 K52 E54 Y64
• Binding residue (residue number reindexed from 1): P1 K2 M3 K4 T5 H6 K7 K11 R12 K14 T16 A17 S18 K20 K25 T26 G27 K28 R29 H30 L31 N32 W33 Q34 G37 K38 R41 Q42 K43 R45 K46 L49 A50 K51 E53 Y63

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:6nta, PDBe:6nta, PDBj:6nta
• PDBsum: 6nta
• PubMed: 33016876
• UniProt: Q5SKU1|RL35_THET8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)