Structure of PDB 4v97 Chain B0 Binding Site BS02

Receptor Information

>4v97 Chain B0 (length=84) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA

Ligand information

>4v97 Chain BA (length=2810)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucgcgaauccccag
ccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgua
ggcgaaagguggggggauaggugaggguacccgaguaccccgugguucgu
ggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacuccg
ggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaaccccg
ggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacgg
ccccgcaagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcccaccag
ccuaccaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cgaagacagccucgaguggcgccgcgccgaaaaugaucggggcuuaagcc
cagcgccgaagcugcgggucugggggaugaccccaggcgguaggggagcg
uucccgaugccgaugaaggccgacccgcgagggcggcuggagguaaggga
agugcgaaugccggcaugaguaacgauaaagagggugagaaucccucucg
ccguaagcccaaggguuccuacgcaauggucgucagcguaggguuaggcg
ggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaauau
uccggcccuucccgcaggugcgauggggggacgcucuaggcuagggggac
cggagccauggacgagcccggccagaagcgcagggugggagguaggcaaa
uccgccucccaacaagcucugcgugguggggaagcccgggugacaacccc
ccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaaccc
guaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcg
ggagaacccucgccaaggaacucugcaaguuggccccguaacuucgggag
aaggggugcucccuggggugaugagccccggggagccgcagugaacaggc
ucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaagagga
gguauagggagcgacgcuugcccggugccggaaggucaaggggaggggug
caagccccgaaccgaagccccggugaacggcggccguaacuauaacgguc
cuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagc
guaacgaccggagcgcugucucggcgagggacccggugaaauugaacugg
ccgugaagaugcggccuacccguggcaggacgaaaagaccccguggagcu
uuacugcagccugguguuggcucuuggucgcgccugcguaggauaggugg
gagccugugaacccccgccuccgggugggggggaggcgccggugaaauac
cacccuggcgcggcugggggccuaacccucggauggggggacagcgcuug
gcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcc
caaagguccccucaggcgggacggaaauccgccggagagcgcaaggguag
aagggggccugacugcgaggccugcaagccgagcaggggcgaaagccggg
ccuagugaaccgguggucccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagcguccacagcggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgccacgggcgcaggagg
cuugaggggggcucuuccuaguacgagaggaccggaagggacgcaccucu
gguuucccagcugucccuccaggggcauaagcuggguagccaugugcgga
agggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugagg
ccucccacggcgucaagccgguaaggacccgggaagaccacccgguggau
gggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucg
uccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v97 Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
• Resolution: 3.516 Å
• Binding residue (original residue number in PDB): H3 K4 G8 S9 T10 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 A33 G34 N35 I36 R39 R41 T43 R44 G54 R55 D56 F60 F69 R77
• Binding residue (residue number reindexed from 1): H2 K3 G7 S8 T9 N11 R13 D14 S15 Q16 A17 K18 R19 K23 R24 Y25 E26 Q28 A32 G33 N34 I35 R38 R40 T42 R43 G53 R54 D55 F59 F68 R76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v97, PDBe:4v97, PDBj:4v97
• PDBsum: 4v97
• PubMed: 23630274
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)