Structure of PDB 6qnr Chain 15 Binding Site BS01

Receptor Information

>6qnr Chain 15 (length=138) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKL

Ligand information

>6qnr Chain 14 (length=2876)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuugcgcggggggaaccuggggaacugaaacaucucaguacccaga
ggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggac
cagccuaaaccguccggcuuguccgggcggggucguggggcccucggaca
ccgaauccccagccuagccgaagcuguugggaagcagcgccagagagggu
gaaagccccguaggcgaaagguggggggauaggugaggguacccgaguac
cccgugguucguggagccaugggggaaucugggcggaccaccgccuaagg
cuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuac
aagcagucacggccccgcaagggguuguggcgugccuauugaagcaugag
ccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcgua
gggaaaccgaguccgaacagggcgcaaacggcccgaaaaguccgcggccg
uggacccgaaaccgggcgagcuagcccuggccagggugaagcugggguga
gacccaguggaggcccgaaccggugggggaugcaaaccccucggaugagc
uggggcuaggagugaaaagcuaaccgagcccggagauagcugguucuccc
cgaaaugacuuuagggucagccucaggcgcugacuggggccuguagagca
cugauagggcuagggggcccaccagccuaccaaacccugucaaacuccga
agggucccagguggagccugggagugagggcgcgagcgauaacguccgcg
uccgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucuggg
cuaagugguaaaggauguggcgccgcgaagacagccaggauguugaucau
uuaaagagugcucacuggucgaguggcgccgcgccgaaaaugaucggggc
uuaagcccagcgccgaagcugcgggucugggggaugaccccaggcgguag
gggagcguucccgaugccgaugaaggccgacccgcgagggcggcuggagg
uaagggaagugcgaaugccggcaugaguaacgauaaagagggugagaauc
ccucucgccguaagcccaaggguuccuacgcaauggucgucagcguaggg
uuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgg
uuaauauuccggcccuucccgcaggugcgauggggggacgcucuaggcua
gggggaccggagccauggacgagcccggccagaagcgcagggugggaggu
aggcaaauccgccucccaacaagcucugcgugguggggaagcccguacgg
gugacaaccccccgaagccagggagccaagaaaagccucuaagcacaacc
ugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagagcac
ucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggccccgu
aacuucgggagaaggggugcucccuggggugaugagccccggggagccgc
agugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcgaac
ucguaagaggagguauagggagcgacgcuugcccggugccggaaggucaa
ggggaggggugcaagccccgaaccgaagccccggugaacggcggccguaa
cuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccu
gcacgaaaagcguaacgaccggagcgcugucucggcgagggacccgguga
aauugaacuggccgugaagaugcggccuacccguggcaggacgaaaagac
cccguggagcuuuacugcagccugguguuggcucuuggucgcgccugcgu
aggauaggugggagccugugaacccccgccuccgggugggggggaggcgc
cggugaaauaccacccuggcgcggcugggggccuaacccucggauggggg
gacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaaggua
acggaggcgcccaaagguccccucaggcgggacggaaauccgccggagag
cgcaaggguagaagggggccugacugcgaggccugcaagccgagcagggg
cgaaagccgggccuagugaaccgguggucccguguggaagggccaucgau
caacggauaaaaguuaccccggggauaacaggcugaucucccccgagcgu
ccacagcggcggggagguuuggcaccucgaugucggcucgucgcauccug
gggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggcac
gcgagcuggguucagaacgucgugagacaguucggucucuauccgccacg
ggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaagg
gacgcaccucugguuucccagcugucccuccaggggcauaagcuggguag
ccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgcc
ccaagaugaggccucccacggcgucaagccgguaaggacccgggaagacc
acccgguggaugggccggggguguaagcgccgcgaggcguugagccgacc
ggucccaaucguccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qnr Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K2 T3 V5 W13 G24 R25 T28 K37 N45 F51 T63 G64 K65 K66 Q69 K70 Y72 R74 Y75 S76 Y78 P79 G80 L82 K83 H94 R97 E100 A102 G105 M106 G110 P111 L112 R114 F117 K118 K121 P129 Q131
• Binding residue (residue number reindexed from 1): K2 T3 V5 W13 G24 R25 T28 K37 N45 F51 T63 G64 K65 K66 Q69 K70 Y72 R74 Y75 S76 Y78 P79 G80 L82 K83 H94 R97 E100 A102 G105 M106 G110 P111 L112 R114 F117 K118 K121 P129 Q131

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6qnr, PDBe:6qnr, PDBj:6qnr
• PDBsum: 6qnr
• PubMed: 31175275
• UniProt: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)