Structure of PDB 3pip Chain U Binding Site BS01

Receptor Information
>3pip Chain U (length=72) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRENGQV
KTVWLSANALRTLSKGPYKGIE
Ligand information
>3pip Chain X (length=2644) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaauc
aagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguagg
cgaacgagaggucguuguucgugaaacgaugacugaauccgcgcggacca
ccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugag
ggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccg
uggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauu
gaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaa
cggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucggg
cuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccggg
ggcggaggaccgaaccggugccugcugaaacagucucggaugaguugugu
uuaggagugaaaagcuaaccgaaccuggagauagcuaguucuccccgaaa
uguauugagguacagccucggauguugaccauguccuguagagcacucac
aaggcuaaaccuuaugaaacuccgaaggggcacgcguuuaguccgggagu
gaggcugcgagagcuaacuuccguagccgagagggaaacaacccagacca
ucagcuaaggucccuaaaugaucgcucagugguuaaggaugugucgucgc
gacagccaggagguuggcuuagagcagccacccuucaaagagugcguaau
agcucacuggucgagugacgaugcgccgaaaaugaucggggcucaaguga
ucuaccgaagcuauggauucaacucguugucugguaggggagcguucagu
ccgcggagaagccauaccggaaggagugguggagccgacugaagugcgga
ugccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaagg
acaaggguuccuggggaagggucguccgcccagggaaagucgggaccuaa
ggugaggccgaacggcgcagccgauggacagcaggucaagauuccugcac
cgaucaugugagugauggagggacgcauuacgcuauccaaugccaagcua
uggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuacc
gguugccucagacguaucgggagcuuccucggaagcgaaguuggaaacgc
gacggugccaagaaaagcuucuaaacguugaaacaugauugcccguaccg
caaaccgacacagguguccgagugucaaugcacuaaggcgcgcgagagaa
cccucguuaaggaacuuugcaaucucaccccguaacuucggaagaagggg
uccccacgcuucgcguggggcgcagugaauaggcccaggcgacuguuuac
caaaaucacagcacucugccaacacgaacaguggacuauagggugugacg
ccugcccggugccggaaggucaaguggagcggugcaagcugcgaaaugaa
gccccggugaacggcuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaaaggcguaacgaucugggcgcugucucaacgagggacucgg
ugaaauugaauuggcuguaaagaugcggccuacccguagcaggacgaaaa
gaccccguggagcuuuacuauagucuggcauugggauucgggucuuggau
uucuaaccugaaaaaucacuuucggggaccgugcuuggcggguaguuuga
cuggggcggucgccucccaaaauguaacggaggcgcccaaaggucaccuc
aagacgguuggaaaucgucuguagagcgcaaagguagaagguggcuugac
ugcgagacugacacgucgagcagggaggaaacucgggcuuagugaaccgg
ugguaccguguggaagggccaucgaucaacggauaaaaguuaccccgggg
auaacaggcugaucucccccgagaguccauaucggcggggagguuuggca
ccucgaugucggcucgucgcauccuggggcugaagaaggucccaaggguu
gggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgug
agacaguucggucucuauccgcuacgggcgcaggagaauugaggggaguu
gcuccuaguacgagaggaccggagugaacggaccgcuggucucccugcug
ucguaccaacggcacaugcaggguagcuauguccggaacggauaaccgcu
gaaagcaucuaagcgggaagccagccccaagaugaguucucccacugagg
uaagacucccggaagaccaccggguuaagaggccaggcgugcacgcauag
caauguguucagcggacuggugcucaucagucgaggucuugacc
<<<<<<<<......<<<<<<<<<<<.....<<..<<.<<<<<<<<<....
..<<<<<<.[...((.>>>.....<<<<<<...<<.))...]..>>....
..>>>>>>...>>>....<<<....>>><<<<<....>>>>><<<<....
>>>>>>...<<<<<<.....<<....>>......>>>>>.>.........
<<....>>...<<<<......<<.....>>.....>>>>...<<<...<<
..<<<...<<<<<......>>>>>((......<<<.....))>>>...>>
>....>>..<<<<<<<<.........>>>>>>>>......<<<<<..<<<
<>>>>>..>>>......>>.>>>>>..>>..............<<....>
>....>>.........<<<<....>>>>..................>>>>
>>>>>>>.......<<<<<<<<<<.......>>>>>>>>>>...<.....
.......>.<<<<<<....<<<.<<<<<<<<<<..<<<...<<<....>>
>...>>>...<<....>>...<........>.........>>>>>>>>>>
>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<.....<<<<..>>
>>......>>>...<<<..<.<<........>>.>.>>>....>>>>>>>
>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<....
<<<<<....>>>>><<<<<<<<<...<<<<.<<<<<<...<<<...<<<.
<<<<.....>>>>.>>>..>>.>...>>>>>>.>.>>>..>>>>>>>.>>
..<<<<<<<.<<......>>.>>>>>>>....<<<......>>>...<<<
<.<<<...<<<(((.....<<<<<<...........<<..<<<<<<<<<.
....<<<<<.<<...<<<<......>>>>...>>.......<.<<.....
.>>.>.>>>>>....>>>>>>>>>.>>..........)))......>>>>
>>.>>>...>>>>>>><..<<<<..>>>>..>....>>>>>><<<<<<<<
<.<<......<<<<<.<<....>>.>>>>>...>>.>>>>>>>.>>....
.>>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...
<<<...<<<<..>>>>...>>>...>>...<<<<<........>>>>>))
<<<<<<<<<..<<...<<<<....<<<<..<<<..<<<<<.<<<<.<<..
.[[....>>>>>><<<<<<<.<<..<<<<.<<<<<...<<.....>>.>>
>>>.>>>>..>>>>>>>>>...<<<<<....>>>>>....>>>>>...>>
>...>>>>.........>>>>...>>......>>>>>>>>>>>>>..>>.
....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<....
<<<<<<<<.<<.........<.....<<<<<.....<..>......>>>>
><<<<<<<<...>>>>>>>>............<<<<<<<<<..<<.....
......>>..<<<<<<<.....<<<.....>>>......>>>>>>>.<<<
<<.<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>>...
>>>>>>>>..>>>>>.......<...........<<<<<.......>>>>
>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>
>.....>.....<<<<<........>>>>>..<<<<<<<<.<<<......
...<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<...>>>>>>
>>>...<<<<<<........>>>>>>....>>>>>.>>>..>>>>>..<<
<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<..
.<<<<<<.......>>>>>>.....<....(((.>....>>>>>>>...<
<<<..<<<......>>>..>>>>.<<<....>>>.>>))).......<<<
<<<<.<<..>>>>..>>>>>>>>>.............>>>>..>>>>>>.
......<<<<.<.<<<<<<.<.<<.......>>..>>>>>>>...>>>>.
>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<
<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<...
.>>>.>>>>........>>>>>>>>>>>....<<<<<<<...<<<<..<<
<<<<<...............>>>>>>>.<<<<<....<<<...<<<<<<<
<<<<.]].>>>>>>...>>>>>...>>>..>>>>>....<<.<..<<<<<
...........>>>>>...>>>..>>>>.......>>>>>>>..<<.>>.
...<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<.
...>>>>>...>>>..>>>>>.>>>...>>>>....>>>>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3pip Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
Resolution3.45 Å
Binding residue
(original residue number in PDB)
N16 V18 I19 R20 R21 R32 T35 I37 T38 K39 V41 Q42 R43 A44 N45 L46 H47 K48 K49 I51 R68
Binding residue
(residue number reindexed from 1)
N9 V11 I12 R13 R14 R25 T28 I30 T31 K32 V34 Q35 R36 A37 N38 L39 H40 K41 K42 I44 R61
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:3pip, PDBe:3pip, PDBj:3pip
PDBsum3pip
PubMed21282615
UniProtQ9RRG8|RL28_DEIRA Large ribosomal subunit protein bL28 (Gene Name=rpmB)

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