Structure of PDB 3pio Chain B Binding Site BS01

Receptor Information

>3pio Chain B (length=205) Species: 1299 (Deinococcus radiodurans)

MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIG
YAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGE
KIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRV
YKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRS
AAKAS

Ligand information

>3pio Chain X (length=2657)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaauc
aagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguagg
cgaacgagaggucguuguucgugaaacgaugacugaauccgcgcggacca
ccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugag
ggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccg
uggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauu
gaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaa
cggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucggg
cuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccggg
gggcggaggaccgaaccggugccugcugaaacagucucggaugaguugug
uuuaggagugaaaagcuaaccgaaccuggagauagcuaguucuccccgaa
auguauugagguacagccucggauguugaccauguccuguagagcacuca
caaggcuaaaccuuaugaaacuccgaaggggcacgcguuuaguccgggag
ugaggcugcgagagcuaacuuccguagccgagagggaaacaacccagacc
aucagcuaaggucccuaaaugaucgcucagugguuaaggaugugucgucg
cauagacagccaggagguuggcuuagaagcagccacccuucaaagagugc
guaauagcucacuggucgagugacgaugcgccgaaaaugaucggggcuca
agugaucuaccgaagcuauggauucaacucggaguugucugguaggggag
cguucaguccgcggagaagccauaccggaaggagugguggagccgacuga
agugcggaugccggcaugaguaacgauaaaagaagugagaaucuucuucg
ccguaaggacaaggguuccuggggaagggucguccgcccagggaaagucg
ggaccuaaggugaggccgaacggcgcagccgauggacagcaggucaagau
uccugcaccgaucauguggagugauggagggacgcauuacgcuauccaau
gccaagcuauggcuaugcugguugguacgcucaagggcgaucgggucaga
aaaucuaccggucugccucagacguaucgggagcuuccucggaagcgaag
uuggaaacgcgacggugccaagaaaagcuucuaaacguugaaacaugauu
gcccguaccgcaaaccgacacagguguccgagugucaaugcacuaaggcg
cgcgagagaacccucguuaaggaacuuugcaaucucaccccguaacuucg
gaagaagggguccccacgcuucgcguggggcgcagugaauaggcccaggc
gacuguuuaccaaaaucacagcacucugccaacacgaacaguggacguau
agggugugacgccugcccggugccggaaggucaaguggagcggugcaagc
ugcgaaaugaagccccggugaacggcuaagguagcgaaauuccuugucgg
guaaguuccgaccugcacgaaaggcguaacgaucugggcgcugucucaac
gagggacucggugaaauugaauuggcuguaaagaugcggccuacccguag
caggacgaaaagaccccguggagcuuuacuauagucuggcauugggauuc
ggguuacuuggauuucuaaccugaaaaaucacuuucggggaccgugcuug
gcggguaguuugacuggggcggucgccucccaaaauguaacggaggcgcc
caaaggucaccucaagacgguuggaaaucgucuguagagcgcaaagguag
aagguggcuugacugcgagacugacacgucgagcagggaggaaacucggg
cuuagugaaccggugguaccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagaguccauaucggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgcuacgggcgcaggaga
auugaggggaguugcuccuaguacgagaggaccggagugaacggaccgcu
ggucucccugcugucguaccaacggcacaugcaggguagcuauguccgga
acggauaaccgcugaaagcaucuaagcgggaagccagccccaagaugagu
ucucccacugagguaagacucccggaagaccaccggguuaagaggccagg
cgugcacgcauagcaauguguucagcggacuggugcucaucagucgaggu
cuugacc

.<<<<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<....
..<<<<<<.((..((.>>>.....<<<<<<...<<.))..))..>>....
..>>>>>>...>>>....<<<....>>><<<<<....>>>>><<<<....
>>>>>>...<<<<<<.....<<....>>......>>>>>.>.........
<<....>>...<<<<......<<.....>>.....>>>>...<<<...<<
..<<<...<<<<<......>>>>>((......<<<.....))>>>...>>
>....>>..<<<<<<<<.........>>>>>>>>......<<<<<..(((
(>>>>>..>>>......>>.>>>>>>.>>..............<<....>
>....>>.........<<<<....>>>>..................>>>>
>>>>>>>.......<<<<<<<<<<.......>>>>>>>>>>...<.....
.......>.<<<<<<....<<<.<<<<<<<<<<..<<<...<<<....>>
>...>>>...<<....>>...<........>.........>>>>>>>>>>
>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<.....<<<<<.>>
>>>......>>>...<<<..<.<<........>>.>.>>>....>>>>>>
>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<...
.<<<<<....>>>>><<<<<<<<<...<<<<.<<<<<<...<<<...<<<
.<<<<.....>>>>.>>>..>>.>...>>>>>>.>.>>>..>>>>>>>.>
>..<<<<<<<.<<......>>.>>>>>>>....<<<......>>>...<<
<<.<<<...<<<(((.....<<<<<<...........<<..<<<<<<<<<
........<<<<<.<<...<<<<.......>>>>...>>.........<<
......>>...>>>>>....>>>>>>>>>.>>..........))).....
.>>>>>>.>>>...>>>>>>><..<<<<.....>>>>..>....>>>>>>
<.<<<<<<<.<<......<<<<<.<<....>>.>>>>>...>>.>>>>>>
>..>.....>>>>>><......<<.....<<<<<<.......>>>>>><<
<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<
<<.<<...<<<...<<<<..>>>>...>>>...>>...<<<<<.......
.>>>>>))<<<<<<<<<...<<...<<<<....<<<<..<<<..<<<<<.
<<<<.<<...[[....>>>>>><<<<<<<.<<..<<<.<<<<<<...<<.
....>>.>>>>>>..>>>..>>>>>>>>>...<<<<<....>>>>>....
>>>>>...>>>...>>>>.........>>>>...>>......>>>>>>>>
>>>>>..>>.....<<......>>>>>>>.<<<<<....>>>>>..>>>>
..<<<<....<<<<<<<<.<<.........<.....<<<<<....<<..>
>.....>>>>><<<<<<<<...>>>>>>>>............<<<<<<<<
<..<<...........>>..<<<<<<<.....<<<.....>>>.......
>>>>>>>.<<<<<..<<..<<<<<<<..<<<...<<...<<<<<....>>
>>>...>>...>>>>>>>>..>>>>........<...........<<<<<
.......>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>
>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<
<.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<<
<<<<.>>>>>>>>>>>...<<<<<<........>>>>>>....>>>>>.>
>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<....(((.>..
..>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>
))).......<<<<<<<.<<..))))..>>>>>>>>>.............
>>>>..>>>>>>.......<<<<.<.<<<<<<...<<.......>>...>
>>>>>...>>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......
>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>.
...<<<<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<<
<<...<<<<..<<<<<<<...............>>>>>>>.<<<<<....
<<<...<<<<<<<<<<<.]].>>>>>>...>>>>>...>>>..>>>>>..
..<<....<<<<<...........>>>>>....>>..>>>>.......>>
>>>>>..<<.>>....<<<<<<<<<.......>>>>>....<<<<<<<<.
<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>....>
>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3pio Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
• Resolution: 3.2473 Å
• Binding residue (original residue number in PDB): K8 M11 T12 Q13 P22 Q35 D42 Y44 Q48 R57 K58 N60 K61 P62 M63 G65 H66 K69 R79 E80 R82 S108 K109 G110 K111 G112 T113 Q114 G115 K118 R119 F122 A123 P126 A127 S128 H129 G130 K133 W134 R136 R137 P138 G139 S140 I141 G142 Q143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 M156 A157 H159 M162 R164 T166 Q168 N169 G186 A187 I188 P189 G190 A191 N192 K203
• Binding residue (residue number reindexed from 1): K8 M11 T12 Q13 P22 Q35 D42 Y44 Q48 R57 K58 N60 K61 P62 M63 G65 H66 K69 R79 E80 R82 S108 K109 G110 K111 G112 T113 Q114 G115 K118 R119 F122 A123 P126 A127 S128 H129 G130 K133 W134 R136 R137 P138 G139 S140 I141 G142 Q143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 G153 M156 A157 H159 M162 R164 T166 Q168 N169 G186 A187 I188 P189 G190 A191 N192 K203

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

External links

• PDB: RCSB:3pio, PDBe:3pio, PDBj:3pio
• PDBsum: 3pio
• PubMed: 21282615
• UniProt: Q9RXK2|RL3_DEIRA Large ribosomal subunit protein uL3 (Gene Name=rplC)