Structure of PDB 5dm6 Chain G Binding Site BS01

Receptor Information

>5dm6 Chain G (length=142) Species: 1299 (Deinococcus radiodurans)

KTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDF
VVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEH
AVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPL

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): K30 T31 I33 W41 P50 L51 G52 R53 T56 K65 N73 F79 T91 K94 K98 R102 Y103 T104 Y106 Q107 L110 K121 H122 R125 E128 A130 G133 M134 R139 Q140 R142 P157 H158 A160 Q161 K162
• Binding residue (residue number reindexed from 1): K1 T2 I4 W12 P21 L22 G23 R24 T27 K36 N44 F50 T62 K65 K69 R73 Y74 T75 Y77 Q78 L81 K92 H93 R96 E99 A101 G104 M105 R110 Q111 R113 P128 H129 A131 Q132 K133

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:5dm6, PDBe:5dm6, PDBj:5dm6
• PDBsum: 5dm6
• PubMed: 26464437
• UniProt: Q9RXY1|RL13_DEIRA Large ribosomal subunit protein uL13 (Gene Name=rplM)