Structure of PDB 5dox Chain 2U Binding Site BS01

Receptor Information

>5dox Chain 2U (length=116) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQ

Ligand information

>5dox Chain 2A (length=2867)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucuggggccccaggcg
guaggggagcguucccgaugccgaugaaggccgacccgcgagggcggcug
gagguaagggaagugcgaaugccggcaugaguaacgauaaagagggugag
aaucccucucgccguaagcccaaggguuccuacgcaauggucgucagcgu
aggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcag
ccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucuag
gcuagggggaccggagccauggacgagcccggccagaagcgcaggguggg
agguaggcaaauccgccucccaacaagcucugcgugguggggaagcccgc
gggugacaaccccccgaagccagggagccaagaaaagccucuaagcacaa
ccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagagc
acucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcccc
guaacuucgggagaaggggugcucccuggggugaugagccccggggagcc
gcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcga
acucguaagaggagguauagggagcgacgcuugcccggugccggaagguc
aaggggaggggugcaagccccgaaccgaagccccggugaacggcggccgu
aacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgac
cugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccggu
gaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaag
accccguggagcuuuacugcagccugguguuggcucuuggucgcgccugc
guaggauaggugggagccugugaacccccgccuccgggugggggggaggc
gccggugaaauaccacccuggcgcggcugggggccuaacccucggauggg
gggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagg
uaacggaggcgcccaaagguccccucaggcgggacggaaauccgccggag
agcgcaaggguagaagggggccugacugcgaggccugcaagccgagcagg
ggcgaaagccgggccuagugaaccgguggucccguguggaagggccaucg
aucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagc
guccacagcggcggggagguuuggcaccucgaugucggcucgucgcaucc
uggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggc
acgcgagcuggguucagaacgucgugagacaguucggucucuauccgcca
cgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaa
gggacgcaccucugguuucccagcugucccuccaggggcauaagcugggu
agccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccg
ccccaagaugaggccucccggcagccgguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dox Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 R3 A4 K5 T6 G7 V8 V9 R10 R11 R12 K13 H14 K15 K16 K19 K22 G23 Y24 W25 G26 L27 R28 K30 S31 F32 R33 K34 R36 E37 A42 Y45 Y47 H49 R50 K51 R52 R53 K54 R55 F57 R58 R59 W61 I62 N66 R70 N75 Y76 S77 I80 H81 D91 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 G6 V7 V8 R9 R10 R11 K12 H13 K14 K15 K18 K21 G22 Y23 W24 G25 L26 R27 K29 S30 F31 R32 K33 R35 E36 A41 Y44 Y46 H48 R49 K50 R51 R52 K53 R54 F56 R57 R58 W60 I61 N65 R69 N74 Y75 S76 I79 H80 D90 R91 K92

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5dox, PDBe:5dox, PDBj:5dox
• PDBsum: 5dox
• PubMed: 26028538
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)