Structure of PDB 6ord Chain YW Binding Site BS01

Receptor Information

>6ord Chain YW (length=112) Species: 300852 (Thermus thermophilus HB8)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHG

Ligand information

>6ord Chain YA (length=2867)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucuggggccccaggcg
guaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcug
gagguaagggaagugcgaaugccggcaugaguaacgauaaagagggugag
aaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcgu
aggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcag
ccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucuag
gcuagggggaccggagccauggacgagcccggccagaagcgcaggguggg
agguaggcaaauccgccucccaacaagcucugcgugguggggaagcccgc
gggugacaaccccccgaagccagggagccaagaaaagccucuaagcacaa
ccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagagc
acucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcccc
guaacuucgggagaaggggugcucccuggggugaugagccccggggagcc
gcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcga
acucguaagaggagguauagggagcgacgcuugcccggugccggaagguc
aaggggaggggugcaagccccgaaccgaagccccggugaacggcggccgu
aacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgac
cugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccggu
gaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaag
accccguggagcuuuacugcagccugguguuggcucuuggucgcgccugc
guaggauaggugggagccugugaacccccgccuccgggugggggggaggc
gccggugaaauaccacccuggcgcggcugggggccuaacccucggauggg
gggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagg
uaacggaggcgcccaaagguccccucaggcgggacggaaauccgccggag
agcgcaaggguagaagggggccugacugcgaggccugcaagccgagcagg
ggcgaaagccgggccuagugaaccgguggucccguguggaagggccaucg
aucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagc
guccacagcggcggggagguuuggcaccucgaugucggcucgucgcaucc
uggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggc
acgcgagcuggguucagaacgucgugagacaguucggucucuauccgcca
cgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaa
gggacgcaccucugguuucccagcugucccuccaggggcauaagcugggu
agccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccg
ccccaagaugaggccucccggcagccgguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ord Disruption of evolutionarily correlated tRNA elements impairs accurate decoding.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K4 I6 A7 R8 Y9 R11 S13 R15 K16 N40 K41 R42 Y45 K49 E52 S53 A56 N57 N60 N61 H62 D77 E78 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99
• Binding residue (residue number reindexed from 1): K4 I6 A7 R8 Y9 R11 S13 R15 K16 N40 K41 R42 Y45 K49 E52 S53 A56 N57 N60 N61 H62 D77 E78 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ord, PDBe:6ord, PDBj:6ord
• PDBsum: 6ord
• PubMed: 32601241
• UniProt: Q5SHP3|RL22_THET8 Large ribosomal subunit protein uL22 (Gene Name=rplV)