Structure of PDB 1y69 Chain K Binding Site BS01

Receptor Information

>1y69 Chain K (length=136) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVM
SRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMF
EVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEA

Ligand information

>1y69 Chain 0 (length=2766)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaau
ucaaccccucaagccgaaguggcuggaaagcuacaccucagaaggugaga
guccuguaggcgaacgagcgguugacuguaaggucguuguucgugaaacg
augacugaauccgcgcggaccaccgcgcaaggcuaaauacucccagugac
cgauagcgcauaguaccgugagggaaaggugaaaagaaccccgggagggg
agugaaagagaaccugaaaccguggacuuacaagcagucauggcaccuua
ugcguguuauggcgugccuauugaagcaugagccggcgacuuagaccuga
cgugcgagcuuaaguugaaaaacggaggcggagcgaaagcgaguccgaau
agggcggcauuaguacgucgggcuagacucgaaaccaggugagcuaagca
ugaccagguugaaacccccgugacagggggcggaggaccgaaccggugcc
ugcugaaacagucucggaugaguuguguuuaggagugaaaagcuaaccga
accuggagauagcuaguucuccccgaaauguauugagguacagccucgga
uguugaccauguccuguagagcacucacaaggcuaaaaccuuaugaaacu
ccgaaggggcacgcguuuaguccgggagugaggcugcgagagcuaacuuc
cguagccgagagggaaacaacccagaccaucagcuaaggucccuaaauga
ucgcucagugguuaaggaugugucgucgcauagacagccaggagguuggc
uuagaagcagccacccuucaaagagugcguaauagcucacuggucgagug
acgaugcgccgaaaaugaucggggcucaagugaucuaccgaagcuaugga
uucaacucgcgaagcgaguugucugguaggggagcguucaguccgcggag
aagccauaccggaaggagugguggagccgacugaagugcggaugccggca
ugaguaacgauaaaagaagugagaaucuucuucgccguaaggacaagggu
uccuggggaagggucguccgcccagggaaagucgggaccuaaggugaggc
cgaacggcgcagccgauggacagcaggucaagauuccugcaccgaucaug
uggagugauggagggacgcauuacgcuauccaaugccaagcuauggcuau
gcugguugguacgcucaagggcgaucgggucagaaaaucuaccggucaca
ugccucagacguaucgggagcuuccucggaagcgaaguuggaaacgcgac
ggugccaagaaaagcuucuaaacguugaaacaugauugcccguaccgcaa
accgacacagguguccgagugucaaugcacuaaggcgcgcgagagaaccc
ucguuaaggaacuuugcaaucucaccccguaacuucggaagaaggggucc
ccacgcuucgcguggggcgcagugaauaggcccaggcgacuguuuaccaa
aaucacagcacucugccaacacgaacaguggacguauagggugugacgcc
ugcccggugccggaaggucaaguggagcggugcaagcugcgaaaugaagc
cccggugaacggcggccguaacuauaacgguccuaagguagcgaaauucc
uugucggguaaguuccgaccugcacgaaaggcguaacgaucugggcgcug
ucucaacgagggacucggugaaauugaauuggcuguaaagaugcggccua
cccguagcaggacgaaaagaccccguggagcuuuacuauagucuggcauu
gggauucggguuucucugcguaggugggagaaacuggccggucgguggcc
acccugagaaacuuggauuucuaaccugaaaaaucacuuucggggaccgu
gcuuggcggguaguuugacuggggcggucgccucccaaaauguaacggag
gcgcccaaaggucaccucaagacgguuggaaaucgucuguagagcgcaaa
gguagaagguggcuugacugcgagacugacacgucgagcagggaggaaac
ucgggcuuagugaaccggugguaccguguggaagggccaucgaucaacgg
auaaaaguuaccccggggauaacaggcugaucucccccgagaguccauau
cggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcug
aagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagc
uggguucagaacgucgugagacaguucggucucuauccgcuacgggcgca
ggagaauugaggggaguugcuccuaguacgagaggaccggagugaacgga
ccgcuggucucccugcugucguaccaacggcacaugcaggguagcuaugu
ccggaacggauaaccgcugaaagcaucuaagcgggaagccagccccaaga
ugaguucucccacuguucagguaagacucccggaagaccaccggguuaag
aggccaggcgugcacgcauagcaauguguucagcggacuggugcucauca
gucgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1y69 X-ray crystallography on ribosome recycling: mechanism of binding and action of RRF on the 50S ribosomal subunit
• Resolution: 3.33 Å
• Binding residue (original residue number in PDB): R11 K12 Q13 F14 R15 R17 M18 D21 K23 N46 A50 I53 R60 R61 Y66 I67 R68 F70 K78 E81 R83 M84 G85 K86 G87 K88 H124 K125 E140 A141
• Binding residue (residue number reindexed from 1): R6 K7 Q8 F9 R10 R12 M13 D16 K18 N41 A45 I48 R55 R56 Y61 I62 R63 F65 K73 E76 R78 M79 G80 K81 G82 K83 H119 K120 E135 A136
• Binding affinity: PDBbind-CN: Kd=0.52uM

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:1y69, PDBe:1y69, PDBj:1y69
• PDBsum: 1y69
• PubMed: 15616575
• UniProt: Q9RXJ5|RL16_DEIRA Large ribosomal subunit protein uL16 (Gene Name=rplP)