Structure of PDB 3pio Chain C Binding Site BS01

Receptor Information

>3pio Chain C (length=194) Species: 1299 (Deinococcus radiodurans)

AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQV
SKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQ
LGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLV
TDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEI

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

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

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): H28 R39 R40 T42 S44 T45 R46 R48 Q50 S52 K53 R56 Q61 K62 G63 N66 A67 R68 H69 P75 T76 F77 V78 G79 V82 A83 F84 P86 P88 R89 Y93 T94 P96 R97 Q98 V99 L102 A128 K129 T130 K131 K147 R159 R162 N163 G174 Y178
• Binding residue (residue number reindexed from 1): H27 R38 R39 T41 S43 T44 R45 R47 Q49 S51 K52 R55 Q60 K61 G62 N65 A66 R67 H68 P74 T75 F76 V77 G78 V81 A82 F83 P85 P87 R88 Y92 T93 P95 R96 Q97 V98 L101 A127 K128 T129 K130 K146 R158 R161 N162 G173 Y177

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:3pio, PDBe:3pio, PDBj:3pio
• PDBsum: 3pio
• PubMed: 21282615
• UniProt: Q9RXK1|RL4_DEIRA Large ribosomal subunit protein uL4 (Gene Name=rplD)