Structure of PDB 6xqe Chain 10 Binding Site BS01

Receptor Information

>6xqe Chain 10 (length=83) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL

Ligand information

>6xqe Chain 1A (length=2871)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcagcggccgcaaaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggagguggcuuagaagcagccauccu
uuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaaug
aucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccca
ggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcg
gcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggg
ugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguca
gcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagg
gcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcu
cuaggcuagggggaccggagccauggacgagcccggccagaagcgcaggg
ugggagguaggcaaauccgccucccaacaagcucugcgugguggggaagc
ccgggugacaaccccccgaagccagggagccaagaaaagccucuaagcac
aaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaaga
gcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcc
ccguaacuucgggagaaggggugcucccuggggugaugagccccggggag
ccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugc
gaacucguaagaggagguauagggagcgacgcuugcccggugccggaagg
ucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggcc
guaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccg
accugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccg
gugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaa
agaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccu
gcguaggauaggugggagccugugaacccccgccuccgggugggggggag
gcgccggugaaauaccacccuggcgcggcugggggccuaacccucggaug
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccacggcagccgguaaggacccgggaagacc
acccgguggaugggccggggguguaagcgccgcgaggcguugagccgacc
ggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xqe Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): A2 H3 K4 G8 S9 T10 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 T43 R44 G54 R55 D56 F57 F60 F69 R74 L75 R77
• Binding residue (residue number reindexed from 1): A1 H2 K3 G7 S8 T9 N11 R13 D14 S15 Q16 A17 K18 R19 K23 R24 Y25 E26 Q28 R31 A32 G33 N34 I35 R38 R40 T42 R43 G53 R54 D55 F56 F59 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:6xqe, PDBe:6xqe, PDBj:6xqe
• PDBsum: 6xqe
• PubMed: 32817463
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)