Structure of PDB 3pip Chain N Binding Site BS01

Receptor Information

>3pip Chain N (length=117) Species: 1299 (Deinococcus radiodurans)

PRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRR
NKKRDFRRLWIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAR
EPEAFKALVDASRNARQ

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): P2 R3 A4 K5 T6 I8 R10 R11 R12 R13 H14 K15 K22 F24 W25 S27 R28 K30 Q31 Y32 R33 N34 F36 Q37 L40 N41 A42 Y45 Y47 R48 D49 K53 K54 R55 F57 R58 R59 W61 I62 Q63 N66 N75 Y76 S77 N81 K84 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 I7 R9 R10 R11 R12 H13 K14 K21 F23 W24 S26 R27 K29 Q30 Y31 R32 N33 F35 Q36 L39 N40 A41 Y44 Y46 R47 D48 K52 K53 R54 F56 R57 R58 W60 I61 Q62 N65 N74 Y75 S76 N80 K83 R91 K92

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3pip, PDBe:3pip, PDBj:3pip
• PDBsum: 3pip
• PubMed: 21282615
• UniProt: Q9RSW7|RL20_DEIRA Large ribosomal subunit protein bL20 (Gene Name=rplT)