Structure of PDB 6gsj Chain 39 Binding Site BS01

Receptor Information

>6gsj Chain 39 (length=204) Species: 300852 (Thermus thermophilus HB8)

EVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTK
TRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLP
KKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSE
SVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVF
QNRI

Ligand information

>6gsj Chain 14 (length=2811)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucguggggcccucggacaccgaa
uccccagccuagccgaagcuguugggaagcagcgccagagagggugaaag
ccccguaggcgaaagguggggggauaggugaggguacccgaguaccccgu
gguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaag
uacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaag
aaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagca
gucacggccccgcaagggguuguggcgugccuauugaagcaugagccggc
gacucacggucgugggcgagcuuaagccguugaggcggaggcguagggaa
accgaguccgaacagggcgcaaacggcgaaaaguccgcggccguggaccc
gaaaccgggcgagcuagcccuggccagggugaagcuggggugagacccag
uggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcu
aggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaug
acuuuagggucagccucaggcgcugacuggggccuguagagcacugauag
ggcuaggaccaaacccugucaaacuccgaagggucccagguggagccugg
gagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccga
gaccgccagcuaaggcccccaagucugggcuaagugguaaaggauguggc
gccgcggacauggucgaguggcgccgcgccgaaaaugaucggggcuuaag
cccagcgccgaagcugcgggucugggggaugaccccaggcgguaggggag
cguucccgaugccgaugaaggccgacccgcgagggcggcuggagguaagg
gaagugcgaaugccggcaugaguaacgauaaagagggugagaaucccucu
cgccguaagcccaaggguuccuacgcaauggucgucagcguaggguuagg
cgggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaau
auuccggcccuucccgcaggugcgauggggggacgcucuaggcuaggggg
accggagccauggacgagcccggccagaagcgcagggugggagguaggca
aauccgccucccaacaagcucugcgugguggggaagcccguacgggugac
aaccccccgaagccagggagccaagaaaagccucuaagcacaaccugcgg
gaacccguaccgcaaaccgacacaggugggcgggugcaagagcacucagg
cgcgcgggagaacccucgccaaggaacucugcaaguuggccccguaacuu
cgggagaaggggugcucccuggggugaugagccccggggagccgcaguga
acaggcucuggcgacuguuuaccaaaaacacagcucucugcgaacucgua
agaggagguauagggagcgacgcuugcccggugccggaaggucaagggga
ggggugcaagccccgaaccgaagccccggugaacggcggccguaacuaua
acgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacg
aaaagcguaacgaccggagcgcugucucggcgagggacccggugaaauug
aacuggccgugaagaugcggccuacccguggcaggacgaaaagaccccgu
ggagcuuuacugcagccugguguuggcucuuggucgcgccuguaggauag
gugggagccugugaacccccgccuccgggugggggggaggcgccggugaa
uaccacccuggcgcggcugggggccuaacccucggauggggggacagcgc
uuggcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggc
gcccaaagguccccucaggcgggacggaaauccgccggagagcgcaaggg
uagaagggggccugacugcgaggccugcaagccgagcaggggcgaaagcc
gggccuagugaaccgguggucccguguggaagggccaucgaucaacggau
aaaaguuaccccggggauaacaggcugaucucccccgagcguccacagcg
gcggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaa
gaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcug
gguucagaacgucgugagacaguucggucucuauccgccacgggcgcagg
aggcuugaggggggcucuuccuaguacgagaggaccggaagggacgcacc
ucugguuucccagcugucccuccaggggcauaagcuggguagccaugugc
ggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaug
aggccucccacggcgucaagccgguaaggacccgggaagaccacccggug
gaugggccggggguguaagcgccgcgaggcguugagccgaccggucccaa
ucguccgaggu

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

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): H31 L32 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 K52 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 P81 I82 F83 V84 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 R106 K107 G134 K135 T136 R165 R168 N169 L170 L176 G180 N182 Y184
• Binding residue (residue number reindexed from 1): H29 L30 R36 Q38 L39 K41 R42 R43 R44 T46 A47 S48 T49 K50 T51 R52 G53 V55 A56 Y57 S58 G59 R60 K61 Q65 K66 H67 G69 R70 A71 R72 H73 P79 I80 F81 V82 V87 F88 P90 P92 R93 Y97 T98 P100 K101 K102 R104 K105 G132 K133 T134 R163 R166 N167 L168 L174 G178 N180 Y182

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6gsj, PDBe:6gsj, PDBj:6gsj
• PDBsum: 6gsj
• PubMed: 29931292
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)