Structure of PDB 3pip Chain I Binding Site BS01

Receptor Information

>3pip Chain I (length=134) Species: 1299 (Deinococcus radiodurans)

GSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARL
PKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLA
SGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPE

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): R13 K17 R18 V19 G20 R21 G22 P23 T26 K28 T29 A30 G31 R32 G33 K35 G36 Q37 K38 S39 R40 S41 A43 G44 K45 F49 E50 R55 L56 R59 L60 P61 R63 G64 F65 N66 N67 V74 L98 R100 R101 L109 A110 S126 A127
• Binding residue (residue number reindexed from 1): R3 K7 R8 V9 G10 R11 G12 P13 T16 K18 T19 A20 G21 R22 G23 K25 G26 Q27 K28 S29 R30 S31 A33 G34 K35 F39 E40 R45 L46 R49 L50 P51 R53 G54 F55 N56 N57 V64 L88 R90 R91 L99 A100 S116 A117

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:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3pip, PDBe:3pip, PDBj:3pip
• PDBsum: 3pip
• PubMed: 21282615
• UniProt: Q9RSK9|RL15_DEIRA Large ribosomal subunit protein uL15 (Gene Name=rplO)