Structure of PDB 6qnq Chain M5 Binding Site BS01

Receptor Information

>6qnq Chain M5 (length=64) Species: 300852 (Thermus thermophilus HB8)

PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLA
KPEAERIKLLLPYE

Ligand information

>6qnq Chain 14 (length=2879)

caagaugguaagggcccacgguggaugccucggcacccgagccgaugaag
gacguggcuaccugcgauaagccagggggagccgguagcgggcguggauc
ccuggauguccgaaugggggaacccggccggcgggaacgccggucaccgc
gcuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccgcaagggguuguggcgugccuauugaagcaugagccg
gcgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggg
aaaccgaguccgaacagggcgcaaaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggauguuggcuuagaagcagccauc
auuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaa
ugaucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccc
caggcgguaggggagcguucccgaugccgaugaaggccgacccgcgaggg
cggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagag
ggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucgu
cagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaa
gggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacg
cucuaggcuagggggaccggagccauggacgagcccggccagaagcgcag
ggugggagguaggcaaauccgccucccaacaagcucugcgugguggggaa
gcccguacgggugacaaccccccgaagccagggagccaagaaaagccucu
aagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggu
gcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaag
uuggccccguaacuucgggagaaggggugcucccuggggugaugagcccc
ggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcu
cucugcgaacucguaagaggagguauagggagcgacgcuugcccggugcc
ggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaacg
gcggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaa
guuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgagg
gacccggugaaauugaacuggccgugaagaugcggccuacccguggcagg
acgaaaagaccccguggagcuuuacugcagccugguguuggcucuugguc
gcgccugcguaggauaggugggagccugugaacccccgccuccggguggg
ggggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccu
cggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccuc
cuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaauc
cgccggagagcgcaaggguagaagggggccugacugcgaggccugcaagc
cgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaag
ggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucuc
ccccgagcguccacagcggcggggagguuuggcaccucgaugucggcucg
ucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauu
aaagcggcacgcgagcuggguucagaacgucgugagacaguucggucucu
auccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagag
gaccggaagggacgcaccucugguuucccagcugucccuccaggggcaua
agcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgg
gaagcccgccccaagaugaggccucccacggcagccgguaaggacccggg
aagaccacccgguggaugggccggggguguaagcgccgcgaggcguugag
ccgaccggucccaaucguccgaggucuug

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qnq Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): P2 K3 M4 K5 T6 H7 K8 G9 K12 R13 K15 T17 A18 S19 K21 K26 T27 G28 R30 H31 L32 N33 W34 K36 K39 I41 R42 Q43 K44 K47 L50 A51 K52 P53 E54 R57 Y64
• Binding residue (residue number reindexed from 1): P1 K2 M3 K4 T5 H6 K7 G8 K11 R12 K14 T16 A17 S18 K20 K25 T26 G27 R29 H30 L31 N32 W33 K35 K38 I40 R41 Q42 K43 K46 L49 A50 K51 P52 E53 R56 Y63

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6qnq, PDBe:6qnq, PDBj:6qnq
• PDBsum: 6qnq
• PubMed: 31175275
• UniProt: Q5SKU1|RL35_THET8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)