Structure of PDB 6gsj Chain C8 Binding Site BS01

Receptor Information

>6gsj Chain C8 (length=115) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAA

Ligand information

>6gsj Chain 1H (length=2850)

uaagggcccacgguggaugccucggcacccgagccgaugaaggacguggc
uaccugcgauaagccagggggagccgguagcgggcguggaucccuggaug
uccgaaugggggaacccggccggcgggaacgccggucaccgcgcuuuuug
cgcggggggaaccuggggaacugaaacaucucaguacccagaggagagga
aagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccuaa
accguccggcuuguccgggcggggucguggggcccucggacaccgaaucc
ccagccuagccgaagcuguugggaagcagcgccagagagggugaaagccc
cguaggcgaaagguggggggauaggugaggguacccgaguaccccguggu
ucguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguac
uccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaac
cccgggaggggagugaaauagagccugaaaccgugggcuucaagcaguca
cggccccgcaagggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaaacgggggccgaaaaguccgcggccguggaccc
gaaaccgggcgagcuagcccuggccagggugaagcuggggugagacccag
uggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcu
aggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaug
acuuuagggucagccucaggcgcugacuggggccuguagagcacugauag
ggcuaggcagccucaaacccugucaaacuccgaagggucccagguggagc
cugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaa
ccgagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaug
uggcgccgcgaagacagccaggauguuggcuuagaagcagccaucauuua
aagagugcguaauagcucacuggucgaguggcgccgcgccgaaaaugauc
ggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccaggc
gguaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcu
ggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggguga
gaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcg
uaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggca
gccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucua
ggcuagggggaccggagccauggacgagcccggccagaagcgcagggugg
gagguaggcaaauccgccucccaacaagcucugcgugguggggaagcccg
uacgggugacaaccccccgaagccagggagccaagaaaagccucuaagca
caaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaag
agcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggc
cccguaacuucgggagaaggggugcucccuggggugaugagccccgggga
gccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucug
cgaacucguaagaggagguauagggagcgacgcuugcccggugccggaag
gucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggaccc
ggugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaa
aagaccccguggagcuuuacugcagccugguguuggcucuuggucgcgcc
ugcguaggauaggugggagccuaacccccgccuccggguggggggggcgc
cggugaaauaccacccuggcgcggcugggggccuaacccucggauggggg
gacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaaggua
acggaggcgcccaaagguccccucaggcgggacggaaauccgccggagag
cgcaaggguagaagggggccugacugcgaggccugcaagccgagcagggg
cgaaagccgggccuagugaaccgguggucccguguggaagggccaucgau
caacggauaaaaguuaccccggggauaacaggcugaucucccccgagcgu
ccacagcggcggggagguuuggcaccucgaugucggcucgucgcauccug
gggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggcac
gcgagcuggguucagaacgucgugagacaguucggucucuauccgccacg
ggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaagg
gacgcaccucugguuucccagcugucccuccaggggcauaagcuggguag
ccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgcc
ccaagaugaggccuccguaaggacccgggaagaccacccgguggaugggc
cggggguguaagcgccgcgaggcguugagccgaccggucccaaucguccg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gsj Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 G7 V8 R10 R11 R12 K13 H14 K15 K16 K19 G23 Y24 W25 G26 L27 R28 K30 S31 F32 R33 K34 R36 E37 A42 Y45 A46 Y47 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 W61 I62 R70 N75 Y76 S77 I80 H81 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 G6 V7 R9 R10 R11 K12 H13 K14 K15 K18 G22 Y23 W24 G25 L26 R27 K29 S30 F31 R32 K33 R35 E36 A41 Y44 A45 Y46 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 W60 I61 R69 N74 Y75 S76 I79 H80 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6gsj, PDBe:6gsj, PDBj:6gsj
• PDBsum: 6gsj
• PubMed: 29931292
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)