Structure of PDB 4v4j Chain m Binding Site BS01

Receptor Information
>4v4j Chain m (length=124) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRK
VAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGV
YDAAGVKDRKKSRSKYGTKKPKEA
Ligand information
>4v4j Chain y (length=1514) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uggagaguuugauccuggcucagggugaacgcuggcggcgugccuaagac
augcaagucgugcgggccgcgggguuuuacuccguggucagcggcggacg
ggugaguaacgcgugggugaccuacccggaagagggggacaacccgggga
aacucgggcuaaucccccauguggacccgccccuugggguguguccaaag
ggcuuugcccgcuuccggaugggcccgcgucccaucagcuaguugguggg
guaauggcccaccaaggcgacgacggguagccggucugagaggauggccg
gccacaggggcacugagacacgggccccacuccuacgggaggcagcaguu
aggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuuggag
gaagaagcccuucgggguguaaacuccugaacccgggacgaaacccccga
ggaggggacugacgguaccgggguaauagcgccggccaacuccgugccag
cagccgcgguaauacggagggcgcgagcguuacccggauucacugggcgu
aaagggcguguaggcggccuggggcgucccaugugaaagaccacggcuca
accgugggggagcgugggauacgcucaggcuagacggugggagagggugg
uggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccg
auggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcg
uggggagcaaaccggauuagauacccggguaguccacgcccuaaacgaug
cgcgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcgc
gccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacggg
ggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaaga
accuuaccaggccuugacaugcuagggaacccgggugaaagccuggggug
ccccgcgaggggagcccuagcacaggugcugcauggccgucgucagcucg
ugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccguu
aguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcg
ggaggaaggaggggacgacgucuggucagcauggcccuuacggccugggc
gacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacggg
gagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccg
accccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcggu
gaauacguucccgggccuuguacacaccgcccgucacgccaugggagcgg
gcucuacccgaagucgccgggagccuacgggcaggcgccgaggguagggc
ccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcggc
uggaucaccuccuu
....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<......<<<
.<<<..<<<..<<..<<<<<<<<<.....>>>>>>>>>..>>>>>.....
.<<.......<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<...
...>>>>>.....>>>>>....<<<<.<<<<<....>>>>>.>>>>...<
<<<...>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<
.......>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>
>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>
......<<.<<<....<<<<....>>>>..>>>>>.>.>>>>>>..<<<<
......<<<<<..>>>>>.....>>>>....<<<<<........<<<<..
...>>>>..........>>>>>......<<<<<(((...<<<<<.....<
<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........<<<((
.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<....
.>>>>>>....>>>>>>>>>..>>>>>>>>...<<<<<<<<...<<<<<<
<....<<<<<<<....<<<......>>>.......>>>>>>>........
...<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<
<<<...<<...<<<<.........>>>>...>>>>>>>>..........<
<<<<<..<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>
>>.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<
<<<<<<..<.<<<<<<..<<<<<<<<<<......<<........>>....
......<<<<<<<......<<<<<<<<..<<<<<<<....>>>>>>>...
<<<<....>>>>..>>>>>>>>.<<<.<<....<<<<<.......<<<<<
<<<<....>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<
<<..<<<..<<<.....>>>>>>...>>>>>>>.....<<<<<....>>>
>>........>>>>.........>>>...>>..>>>>>...>>>>>>>..
.>>.>>>>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>
..>>....>>>.....>>>>>>>......<..<<.<<<<<<........>
>>>>>>>...>.....>>>>>>.....<<<<<<..........>>>>>>.
......>....>>>>>>>>>>.>>.......<<.<.<<<<.<<<..<<<<
<<<<<<<<<...<.<<<<....<<<....>>>.>>>>.>..>>>>>>>>>
>>>>..>>>.>>>>..>.>>.........<<<<<<<<<....>>>>>>>>
>.............
Receptor-Ligand Complex Structure
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PDB4v4j Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
Resolution3.83 Å
Binding residue
(original residue number in PDB)		P4 T5 N7 Q8 R11 R14 E15 K16 R18 K19 K20 K22 P30 F31 R32 R33 P47 N48 S49 A50 L51 R52 T60 G71 E72 R85 K90 D91 P93 R96 K114 R116 S117 T121
Binding residue
(residue number reindexed from 1)		P1 T2 N4 Q5 R8 R11 E12 K13 R15 K16 K17 K19 P27 F28 R29 R30 P44 N45 S46 A47 L48 R49 T57 G68 E69 R82 K87 D88 P90 R93 K111 R113 S114 T118
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4v4j, PDBe:4v4j, PDBj:4v4j
PDBsum4v4j
PubMed17940016
UniProtQ5SHN3|RS12_THET8 Small ribosomal subunit protein uS12 (Gene Name=rpsL)

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