Structure of PDB 2ogm Chain B Binding Site BS01

Receptor Information

>2ogm Chain B (length=205) Species: 1299 (Deinococcus radiodurans)

MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIG
YAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGE
KIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRV
YKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRS
AAKAS

Ligand information

>2ogm Chain 0 (length=2766)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaau
ucaaccccucaagccgaaguggcuggaaagcuacaccucagaaggugaga
guccuguaggcgaacgagcgguugacuguaaggucguuguucgugaaacg
augacugaauccgcgcggaccaccgcgcaaggcuaaauacucccagugac
cgauagcgcauaguaccgugagggaaaggugaaaagaaccccgggagggg
agugaaagagaaccugaaaccguggacuuacaagcagucauggcaccuua
ugcguguuauggcgugccuauugaagcaugagccggcgacuuagaccuga
cgugcgagcuuaaguugaaaaacggaggcggagcgaaagcgaguccgaau
agggcggcauuaguacgucgggcuagacucgaaaccaggugagcuaagca
ugaccagguugaaacccccgugacagggggcggaggaccgaaccggugcc
ugcugaaacagucucggaugaguuguguuuaggagugaaaagcuaaccga
accuggagauagcuaguucuccccgaaauguauugagguacagccucgga
uguugaccauguccuguagagcacucacaaggcuaaaaccuuaugaaacu
ccgaaggggcacgcguuuaguccgggagugaggcugcgagagcuaacuuc
cguagccgagagggaaacaacccagaccaucagcuaaggucccuaaauga
ucgcucagugguuaaggaugugucgucgcauagacagccaggagguuggc
uuagaagcagccacccuucaaagagugcguaauagcucacuggucgagug
acgaugcgccgaaaaugaucggggcucaagugaucuaccgaagcuaugga
uucaacucgcgaagcgaguugucugguaggggagcguucaguccgcggag
aagccauaccggaaggagugguggagccgacugaagugcggaugccggca
ugaguaacgauaaaagaagugagaaucuucuucgccguaaggacaagggu
uccuggggaagggucguccgcccagggaaagucgggaccuaaggugaggc
cgaacggcgcagccgauggacagcaggucaagauuccugcaccgaucaug
uggagugauggagggacgcauuacgcuauccaaugccaagcuauggcuau
gcugguugguacgcucaagggcgaucgggucagaaaaucuaccggucaca
ugccucagacguaucgggagcuuccucggaagcgaaguuggaaacgcgac
ggugccaagaaaagcuucuaaacguugaaacaugauugcccguaccgcaa
accgacacagguguccgagugucaaugcacuaaggcgcgcgagagaaccc
ucguuaaggaacuuugcaaucucaccccguaacuucggaagaaggggucc
ccacgcuucgcguggggcgcagugaauaggcccaggcgacuguuuaccaa
aaucacagcacucugccaacacgaacaguggacguauagggugugacgcc
ugcccggugccggaaggucaaguggagcggugcaagcugcgaaaugaagc
cccggugaacggcggccguaacuauaacgguccuaagguagcgaaauucc
uugucggguaaguuccgaccugcacgaaaggcguaacgaucugggcgcug
ucucaacgagggacucggugaaauugaauuggcuguaaagaugcggccua
cccguagcaggacgaaaagaccccguggagcuuuacuauagucuggcauu
gggauucggguuucucugcguaggugggagaaacuggccggucgguggcc
acccugagaaacuuggauuucuaaccugaaaaaucacuuucggggaccgu
gcuuggcggguaguuugacuggggcggucgccucccaaaauguaacggag
gcgcccaaaggucaccucaagacgguuggaaaucgucuguagagcgcaaa
gguagaagguggcuugacugcgagacugacacgucgagcagggaggaaac
ucgggcuuagugaaccggugguaccguguggaagggccaucgaucaacgg
auaaaaguuaccccggggauaacaggcugaucucccccgagaguccauau
cggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcug
aagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagc
uggguucagaacgucgugagacaguucggucucuauccgcuacgggcgca
ggagaauugaggggaguugcuccuaguacgagaggaccggagugaacgga
ccgcuggucucccugcugucguaccaacggcacaugcaggguagcuaugu
ccggaacggauaaccgcugaaagcaucuaagcgggaagccagccccaaga
ugaguucucccacuguucagguaagacucccggaagaccaccggguuaag
aggccaggcgugcacgcauagcaauguguucagcggacuggugcucauca
gucgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ogm Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): G65 G110 G115 G139 S140 R144 G148 P189
• Binding residue (residue number reindexed from 1): G65 G110 G115 G139 S140 R144 G148 P189
• Binding affinity: PDBbind-CN: Kd=11.1nM

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:2ogm, PDBe:2ogm, PDBj:2ogm
• PDBsum: 2ogm
• PubMed: 17360517
• UniProt: Q9RXK2|RL3_DEIRA Large ribosomal subunit protein uL3 (Gene Name=rplC)