Structure of PDB 3pip Chain A Binding Site BS01

Receptor Information

>3pip Chain A (length=253) Species: 1299 (Deinococcus radiodurans)

DFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKR
RDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNA
GPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKE
SDYVIVRLPSGELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKP
HQRGSAMNPVDHPHGGGEGRTGAGRVPVTPWGKPTKGLKTRRKRKTSDRF
IVT

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): D21 F22 S23 P39 K40 T41 G42 G43 R44 N45 N46 R47 G48 R49 I50 T51 R53 G56 H59 K60 R61 L62 Y63 K73 V76 P87 H97 D100 G101 E102 K103 K152 Q155 A157 R158 S159 A160 Y173 L178 P179 S180 E182 R184 E189 E201 H202 V206 G208 K209 A210 R212 R214 W215 R218 K219 P220 Q222 R223 G224 S225 A226 M227 N228 P229 V230 D231 H234 G236 G237 E238 R240 G242 R245 T249 P250 K253 P254 T255 K256 G257 L258 K259 R261 R262 K263 R264
• Binding residue (residue number reindexed from 1): D1 F2 S3 P19 K20 T21 G22 G23 R24 N25 N26 R27 G28 R29 I30 T31 R33 G36 H39 K40 R41 L42 Y43 K53 V56 P67 H77 D80 G81 E82 K83 K132 Q135 A137 R138 S139 A140 Y153 L158 P159 S160 E162 R164 E169 E181 H182 V186 G188 K189 A190 R192 R194 W195 R198 K199 P200 Q202 R203 G204 S205 A206 M207 N208 P209 V210 D211 H214 G216 G217 E218 R220 G222 R225 T229 P230 K233 P234 T235 K236 G237 L238 K239 R241 R242 K243 R244

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• 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: Q9RXJ9|RL2_DEIRA Large ribosomal subunit protein uL2 (Gene Name=rplB)