Structure of PDB 6q95 Chain L Binding Site BS01

Receptor Information

>6q95 Chain L (length=146) Species: 300852 (Thermus thermophilus HB8)

DLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGG
RSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAG
LLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Ligand information

>6q95 Chain 1 (length=2831)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucgggggcccucggccgaaucccca
gccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgu
aggcgaaagguggggggauaggugaggguacccgaguaccccgugguucg
uggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacucc
gggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacccc
gggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacg
gccccaagggguuguggcgugccuauugaagcaugagccggcgacucacg
gucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgaguc
cgaacagggcgcguccgcggccguggacccgaaaccgggcgagcuagccc
uggccagggugaagcuggggugagacccaguggaggcccgaaccgguggg
ggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaaccga
gcccggagauagcugguucuccccgaaaugacuuuagggucagccucagg
cgcugacuggggccuguagagcacugauagggcuagggggcgccuaccaa
acccugucaaacuccgaagggucccagguggagccugggagugagggcgc
gagcgauaacguccgcguccgagcgcgggaacaaccgagaccgccagcua
aggcccccaagucugggcuaagugguaaaggauguggcgccgcgaagaca
gccaggagguuggcuuagaagcagccauccuuuaaagagugcguaauagc
ucacuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagc
gccgaagcugcgggucugggggaugaccccaggcgguaggggagcguucc
cgaugccgaugaaggccgacccgcgagggcggcuggagguaagggaagug
cgaaugccggcaugaguaacgauaaagagggugagaaucccucucgccgu
aagcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggac
cuaaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccg
gcccuucccgcaggugcgauggggggacgcucuaggcuagggggaccgga
gccauggacgagcccggccagaagcgcagggugggagguaggcaaauccg
ccucccaacaagcucugcgugguggggaagcccguacgggugacaacccc
ccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaaccc
guaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcg
ggagaacccucgccaaggaacucugcaaguuggccccguaacuucgggag
aaggggugcucccuggggugaugagccccggggagccgcagugaacaggc
ucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaagagga
gguauagggagcgacgcuugcccggugccggaaggucaaggggaggggug
caagccccgaaccgaagccccggugaacggcggccguaacuauaacgguc
cuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagc
guaacgaccggagcgcugucucggcgagggacccggugaaauugaacugg
ccgugaagaugcggccuacccguggcaggacgaaaagaccccguggagcu
uuacugcagccugguguuggcucuuggucgcgccugcguaggauaggugg
gagccuggcgccggugaaauccacccuggcgcggcugggggccuaacccu
cggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccuc
cuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaauc
cgccggagagcgcaaggguagaagggggccugacugcgaggccugcaagc
cgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaag
ggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucuc
ccccgagcguccacagcggcggggagguuuggcaccucgaugucggcucg
ucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauu
aaagcggcacgcgagcuggguucagaacgucgugagacaguucggucucu
auccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagag
gaccggaagggacgcaccucugguuucccagcugucccuccaggggcaua
agcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgg
gaagcccgccccaagaugaggccucccacggcgucaagccgguaaggacc
cgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcgu
ugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q95 How a circularized tmRNA moves through the ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): R7 P8 N9 N13 R15 R16 K17 R18 G20 R21 P23 G24 S25 G26 H27 T30 A31 T32 R33 G34 H35 K36 Q38 K39 S40 R41 S42 G43 K46 D47 P48 R50 F51 E52 G53 G54 R55 L59 M60 R61 P63 K64 G66 M67 G69 Q70 V71 P72 G73 E74 K76 R77 Q81 N84 R90 L105 K107 K113 L115 G116 S131 K132 S133
• Binding residue (residue number reindexed from 1): R3 P4 N5 N9 R11 R12 K13 R14 G16 R17 P19 G20 S21 G22 H23 T26 A27 T28 R29 G30 H31 K32 Q34 K35 S36 R37 S38 G39 K42 D43 P44 R46 F47 E48 G49 G50 R51 L55 M56 R57 P59 K60 G62 M63 G65 Q66 V67 P68 G69 E70 K72 R73 Q77 N80 R86 L101 K103 K109 L111 G112 S127 K128 S129

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6q95, PDBe:6q95, PDBj:6q95
• PDBsum: 6q95
• PubMed: 30765567
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)