Structure of PDB 5dm7 Chain 3 Binding Site BS01

Receptor Information

>5dm7 Chain 3 (length=65) Species: 1299 (Deinococcus radiodurans)

PKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLA
KAEWARMKLMLPRGK

Ligand information

>5dm7 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: 5dm7 Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): P2 K3 M4 K5 T6 K8 M9 R13 K15 T17 G18 T19 K21 M23 K26 S27 G28 K29 R30 H31 Q32 N33 T34 D39 I41 R42 K44 K46 K52 A53 E54 R57 R64
• Binding residue (residue number reindexed from 1): P1 K2 M3 K4 T5 K7 M8 R12 K14 T16 G17 T18 K20 M22 K25 S26 G27 K28 R29 H30 Q31 N32 T33 D38 I40 R41 K43 K45 K51 A52 E53 R56 R63

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:5dm7, PDBe:5dm7, PDBj:5dm7
• PDBsum: 5dm7
• PubMed: 26464437
• UniProt: Q9RSW6|RL35_DEIRA Large ribosomal subunit protein bL35 (Gene Name=rpmI)