Structure of PDB 4ioa Chain O Binding Site BS01

Receptor Information

>4ioa Chain O (length=94) Species: 1299 (Deinococcus radiodurans)

IQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKY
TVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGI

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): Q6 T7 R21 V22 R65 K68 Y70 I71 K73 Y74 G77 V78 Q79 Y80 R81 R82 R83 G85 H86 R87 Q88 N89
• Binding residue (residue number reindexed from 1): Q2 T3 R17 V18 R61 K64 Y66 I67 K69 Y70 G73 V74 Q75 Y76 R77 R78 R79 G81 H82 R83 Q84 N85

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4ioa, PDBe:4ioa, PDBj:4ioa
• PDBsum: 4ioa
• PubMed: 23414806
• UniProt: Q9RY64|RL21_DEIRA Large ribosomal subunit protein bL21 (Gene Name=rplU)