Structure of PDB 3pip Chain C Binding Site BS01

Receptor Information

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

AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQV
SKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQ
LGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLV
TDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEI

Ligand information

>3pip Chain X (length=2644)

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

Structure summary

• PDB: 3pip Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): H28 L35 R38 R39 R40 T42 S44 T45 R46 R48 Q50 R56 Q61 K62 G65 N66 R68 H69 V74 P75 T76 F77 V78 G79 V82 F84 P86 P88 R89 Y91 Y93 T94 R97 Q98 V99 K129 T130 K131 I134 R159 R162 N163 V164 G174 V175 N176 Y178
• Binding residue (residue number reindexed from 1): H27 L34 R37 R38 R39 T41 S43 T44 R45 R47 Q49 R55 Q60 K61 G64 N65 R67 H68 V73 P74 T75 F76 V77 G78 V81 F83 P85 P87 R88 Y90 Y92 T93 R96 Q97 V98 K128 T129 K130 I133 R158 R161 N162 V163 G173 V174 N175 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:3pip, PDBe:3pip, PDBj:3pip
• PDBsum: 3pip
• PubMed: 21282615
• UniProt: Q9RXK1|RL4_DEIRA Large ribosomal subunit protein uL4 (Gene Name=rplD)