Structure of PDB 4ioa Chain U Binding Site BS01

Receptor Information

>4ioa Chain U (length=72) Species: 1299 (Deinococcus radiodurans)

TGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRENGQV
KTVWLSANALRTLSKGPYKGIE

Ligand information

>4ioa Chain X (length=2686)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaauc
aagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguagg
cgaacgagaggucguuguucgugaaacgaugacugaauccgcgcggacca
ccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugag
ggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccg
uggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauu
gaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaa
cggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucggg
cuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccgug
acagggggcggaggaccgaaccggugccugcugaaacagucucggaugag
uuguguuuaggagugaaaagcuaaccgaaccuggagauagcuaguucucc
ccgaaauguauugagguacagccucggauguugaccauguccuguagagc
acucacaaggcuaaaaccuuaugaaacuccgaaggggcacgcguuuaguc
cgggagugaggcugcgagagcuaacuuccguagccgagagggaaacaacc
cagaccaucagcuaaggucccuaaaugaucgcucagugguuaaggaugug
ucgucgcauagacagccaggagguuggcuuagaagcagccacccuucaaa
gagugcguaauagcucacuggucgagugacgaugcgccgaaaaugaucgg
ggcucaagugaucuaccgaagcuauggauucaacucgcgaagcgaguugu
cugguaggggagcguucaguccgcggagaagccauaccggaaggaguggu
ggagccgacugaagugcggaugccggcaugaguaacgauaaaagaaguga
gaaucuucuucgccguaaggacaaggguuccuggggaagggucguccgcc
cagggaaagucgggaccuaaggugaggccgaacggcgcagccgauggaca
gcaggucaagauuccugcaccgaucauguggagugauggagggacgcauu
acgcuauccaaugccaagcuauggcuaugcugguugguacgcucaagggc
gaucgggucagaaaaucuaccggucacaugccucagacguaucgggagcu
uccucggaagcgaaguuggaaacgcgacggugccaagaaaagcuucuaaa
cguugaaacaugauugcccguaccgcaaaccgacacagguguccgagugu
caaugcacuaaggcgcgcgagagaacccucguuaaggaacuuugcaaucu
caccccguaacuucggaagaagggguccccacgcuucgcguggggcgcag
ugaauaggcccaggcgacuguuuaccaaaaucacagcacucugccaacac
gaacaguggacguauagggugugacgccugcccggugccggaaggucaag
uggagcggugcaagcugcgaaaugaagccccggugaacggcuaagguagc
gaaauuccuugucggguaaguuccgaccugcacgaaaggcguaacgaucu
gggcgcugucucaacgagggacucggugaaauugaauuggcuguaaagau
gcggccuacccguagcaggacgaaaagaccccguggagcuuuacuauagu
cuggcauugggauucggguuucuagaaacuuggauuucuaaccugaaaaa
ucacuuucggggaccgugcuuggcggguaguuugacuggggcggucgccu
cccaaaauguaacggaggcgcccaaaggucaccucaagacgguuggaaau
cgucuguagagcgcaaagguagaagguggcuugacugcgagacugacacg
ucgagcagggaggaaacucgggcuuagugaaccggugguaccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagaguccauaucggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgcuacgggcgcaggagaauugaggggaguugcuccuaguacgaga
ggaccggagugaacggaccgcuggucucccugcugucguaccaacggcac
augcaggguagcuauguccggaacggauaaccgcugaaagcaucuaagcg
ggaagccagccccaagaugaguucucccacuguuuaucagguaagacucc
cggaagaccaccggguuaagaggccaggcgugcacgcauagcaauguguu
cagcggacuggugcucaucagucgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ioa Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): V18 I19 R20 R21 R32 K33 T34 T35 I37 T38 K39 R40 V41 Q42 N45 L46 H47 K48 A64 N65 R68
• Binding residue (residue number reindexed from 1): V11 I12 R13 R14 R25 K26 T27 T28 I30 T31 K32 R33 V34 Q35 N38 L39 H40 K41 A57 N58 R61

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4ioa, PDBe:4ioa, PDBj:4ioa
• PDBsum: 4ioa
• PubMed: 23414806
• UniProt: Q9RRG8|RL28_DEIRA Large ribosomal subunit protein bL28 (Gene Name=rpmB)