Structure of PDB 5dox Chain 1m Binding Site BS02

Receptor Information

>5dox Chain 1m (length=116) Species: 300852 (Thermus thermophilus HB8)

ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEA
EVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQ
RTRTNARTRKGPRKTV

Ligand information

>5dox Chain 1a (length=1500)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag
uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg
ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu
gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug
gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca
ggggcacugagacacgggccccacuccuacgggaggcagcaguuaggaau
cuuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaa
gcccuucgggguguaaacuccugaacccgggacgaaacccccgacgaggg
gacugacgguaccgggguaauagcgccggccaacuccgugccagcagccg
cgguaauacggagggcgcgagcguuacccggauucacugggcguaaaggg
cguguaggcggccuggggcgucccaugugaaagaccacggcucaaccgug
ggggagcgugggauacgcucaggcuagacggugggagagggugguggaau
ucccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcg
aaggcagccaccugguccacccgugacgcugaggcgcgaaagcgugggga
gcaaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcu
aggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgcc
uggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccg
cacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuua
ccaggccuugacaugcuagggaacccgggugaaagccuggggugccccgc
gaggggagcccuagcacaggugcugcauggccgucgucagcucgugccgu
gagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugc
cagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggagga
aggaggggacgacgucuggucagcauggcccuuacggccugggcgacaca
cgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcua
aucgcaaaaaggugggcccaguucggauuggggucugcaacccgacccca
ugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauac
guucccgggccuuguacacaccgcccgucacgccaugggagcgggcucua
cccgaagucgccgggagccuacgggcaggcgccgaggguagggcccguga
cuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggauc

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

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): R14 V17 Y21 I22 Y23 G24 I25 G26 A28 R29 R44 V74 N77 Y87 R88 R91 H92 L96 P97 R99 G100 Q101 R102 T103 R104 T105 N106 A107 R108 T109 R110 K111 R114 K115 V117
• Binding residue (residue number reindexed from 1): R13 V16 Y20 I21 Y22 G23 I24 G25 A27 R28 R43 V73 N76 Y86 R87 R90 H91 L95 P96 R98 G99 Q100 R101 T102 R103 T104 N105 A106 R107 T108 R109 K110 R113 K114 V116

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5dox, PDBe:5dox, PDBj:5dox
• PDBsum: 5dox
• PubMed: 26028538
• UniProt: P80377|RS13_THET8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)