Structure of PDB 6gsj Chain P8 Binding Site BS01

Receptor Information
>6gsj Chain P8 (length=47) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTPAVR
Ligand information
>6gsj Chain 1H (length=2850) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6gsj Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria.
Resolution2.96 Å
Binding residue
(original residue number in PDB)
M1 K2 R3 T4 W5 Q6 P7 N8 R9 R10 K11 R12 A13 H16 F18 R19 R21 G26 R28 K29 V30 K32 R33 R34 R35 K37 G38 R39 W40 R41
Binding residue
(residue number reindexed from 1)
M1 K2 R3 T4 W5 Q6 P7 N8 R9 R10 K11 R12 A13 H16 F18 R19 R21 G26 R28 K29 V30 K32 R33 R34 R35 K37 G38 R39 W40 R41
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6gsj, PDBe:6gsj, PDBj:6gsj
PDBsum6gsj
PubMed29931292
UniProtP80340|RL34_THET8 Large ribosomal subunit protein bL34 (Gene Name=rpmH)

[Back to BioLiP]