Structure of PDB 5dm6 Chain O Binding Site BS01

Receptor Information

>5dm6 Chain O (length=94) Species: 1299 (Deinococcus radiodurans)

IQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKY
TVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGI

Ligand information

>5dm6 Chain X (length=2780)

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
uggagcggugcaagcugcgaaaugaagccccggugaacggcggccguaac
uauaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccug
cacgaaaggcguaacgaucugggcgcugucucaacgagggacucggugaa
auugaauuggcuguaaagaugcggccuacccguagcaggacgaaaagacc
ccguggagcuuuacuauagucuggcauugggauucggguuucucugcgua
ggauaggugggagccugcgaaacuggccuuuuggggucgguggaggcaac
ggugaaauaccacccugagaaacuuggauuucuaaccugaaaaaucacuu
ucggggaccgugcuuggcggguaguuugacuggggcggucgccucccaaa
auguaacggaggcgcccaaaggucaccucaagacgguuggaaaucgucug
uagagcgcaaagguagaagguggcuugacugcgagacugacacgucgagc
agggaggaaacucgggcuuagugaaccggugguaccguguggaagggcca
ucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccg
agaguccauaucggcggggagguuuggcaccucgaugucggcucgucgca
uccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagc
ggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccg
cuacgggcgcaggagaauugaggggaguugcuccuaguacgagaggaccg
gagugaacggaccgcuggucucccugcugucguaccaacggcacaugcag
gguagcuauguccggaacggauaaccgcugaaagcaucuaagcgggaagc
cagccccaagaugaguucucccacuguuuaucagguaagacucccggaag
accaccggguuaagaggccaggcgugcacgcauagcaauguguucagcgg
acuggugcucaucagucgaggucuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dm6 Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): G8 K10 R21 E23 S24 R65 K68 Y70 K73 Y74 K75 S76 G77 V78 Y80 R81 R82 R83 T84 G85 H86 R87 Q88
• Binding residue (residue number reindexed from 1): G4 K6 R17 E19 S20 R61 K64 Y66 K69 Y70 K71 S72 G73 V74 Y76 R77 R78 R79 T80 G81 H82 R83 Q84

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:5dm6, PDBe:5dm6, PDBj:5dm6
• PDBsum: 5dm6
• PubMed: 26464437
• UniProt: Q9RY64|RL21_DEIRA Large ribosomal subunit protein bL21 (Gene Name=rplU)