Structure of PDB 3pio Chain J Binding Site BS01

Receptor Information

>3pio Chain J (length=136) Species: 1299 (Deinococcus radiodurans)

KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVM
SRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMF
EVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEA

Ligand information

>3pio Chain X (length=2657)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaauc
aagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguagg
cgaacgagaggucguuguucgugaaacgaugacugaauccgcgcggacca
ccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugag
ggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccg
uggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauu
gaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaa
cggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucggg
cuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccggg
gggcggaggaccgaaccggugccugcugaaacagucucggaugaguugug
uuuaggagugaaaagcuaaccgaaccuggagauagcuaguucuccccgaa
auguauugagguacagccucggauguugaccauguccuguagagcacuca
caaggcuaaaccuuaugaaacuccgaaggggcacgcguuuaguccgggag
ugaggcugcgagagcuaacuuccguagccgagagggaaacaacccagacc
aucagcuaaggucccuaaaugaucgcucagugguuaaggaugugucgucg
cauagacagccaggagguuggcuuagaagcagccacccuucaaagagugc
guaauagcucacuggucgagugacgaugcgccgaaaaugaucggggcuca
agugaucuaccgaagcuauggauucaacucggaguugucugguaggggag
cguucaguccgcggagaagccauaccggaaggagugguggagccgacuga
agugcggaugccggcaugaguaacgauaaaagaagugagaaucuucuucg
ccguaaggacaaggguuccuggggaagggucguccgcccagggaaagucg
ggaccuaaggugaggccgaacggcgcagccgauggacagcaggucaagau
uccugcaccgaucauguggagugauggagggacgcauuacgcuauccaau
gccaagcuauggcuaugcugguugguacgcucaagggcgaucgggucaga
aaaucuaccggucugccucagacguaucgggagcuuccucggaagcgaag
uuggaaacgcgacggugccaagaaaagcuucuaaacguugaaacaugauu
gcccguaccgcaaaccgacacagguguccgagugucaaugcacuaaggcg
cgcgagagaacccucguuaaggaacuuugcaaucucaccccguaacuucg
gaagaagggguccccacgcuucgcguggggcgcagugaauaggcccaggc
gacuguuuaccaaaaucacagcacucugccaacacgaacaguggacguau
agggugugacgccugcccggugccggaaggucaaguggagcggugcaagc
ugcgaaaugaagccccggugaacggcuaagguagcgaaauuccuugucgg
guaaguuccgaccugcacgaaaggcguaacgaucugggcgcugucucaac
gagggacucggugaaauugaauuggcuguaaagaugcggccuacccguag
caggacgaaaagaccccguggagcuuuacuauagucuggcauugggauuc
ggguuacuuggauuucuaaccugaaaaaucacuuucggggaccgugcuug
gcggguaguuugacuggggcggucgccucccaaaauguaacggaggcgcc
caaaggucaccucaagacgguuggaaaucgucuguagagcgcaaagguag
aagguggcuugacugcgagacugacacgucgagcagggaggaaacucggg
cuuagugaaccggugguaccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagaguccauaucggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgcuacgggcgcaggaga
auugaggggaguugcuccuaguacgagaggaccggagugaacggaccgcu
ggucucccugcugucguaccaacggcacaugcaggguagcuauguccgga
acggauaaccgcugaaagcaucuaagcgggaagccagccccaagaugagu
ucucccacugagguaagacucccggaagaccaccggguuaagaggccagg
cgugcacgcauagcaauguguucagcggacuggugcucaucagucgaggu
cuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pio Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
• Resolution: 3.2473 Å
• Binding residue (original residue number in PDB): K9 F10 R11 K12 Q13 F14 R15 G16 R17 M18 K23 G24 F30 N46 Q47 R60 R68 F70 K77 K78 E81 T82 R83 M84 K86 G87 K88 H124 K125 P127 Q129
• Binding residue (residue number reindexed from 1): K4 F5 R6 K7 Q8 F9 R10 G11 R12 M13 K18 G19 F25 N41 Q42 R55 R63 F65 K72 K73 E76 T77 R78 M79 K81 G82 K83 H119 K120 P122 Q124

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:3pio, PDBe:3pio, PDBj:3pio
• PDBsum: 3pio
• PubMed: 21282615
• UniProt: Q9RXJ5|RL16_DEIRA Large ribosomal subunit protein uL16 (Gene Name=rplP)