Structure of PDB 6tbv Chain L321 Binding Site BS01

Receptor Information

>6tbv Chain L321 (length=56) Species: 83333 (Escherichia coli K-12)

AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRG
RKVIAK

Ligand information

>6tbv Chain 23S1 (length=2897)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauguguaggauaggugggaggcuuugaaguguggacgccagucugcaug
gagccgaccuugaaauaccacccuuuaauguuugauguucuaacguugac
ccguaauccggguugcggacagugucugguggguaguuugacuggggcgg
ucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugguc
ggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgu
gacggcgcgagcaggugcgaaagcaggucauagugauccggugguucuga
auggaagggccaucgcucaacggauaaaagguacuccggggauaacaggc
ugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugu
cggcucaucacauccuggggcugaaguaggucccaaggguauggcuguuc
gccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguuc
ggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagu
acgagaggaccggaguggacgcaucacugguguucggguugucaugccaa
uggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucu
aagcacgaaacuugccccgagaugaguucucccugacccuuuaagggucc
ugaaggaacguugaagacgacgacguugauaggccggguguguaagcgca
gcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tbv Ornithine capture by a translating ribosome controls bacterial polyamine synthesis.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): A2 V3 Q4 Q5 N6 K7 T9 R10 S11 R13 G14 M15 R16 R17 S18 H19 S27 S29 V30 R40 H41 Y49 R50
• Binding residue (residue number reindexed from 1): A1 V2 Q3 Q4 N5 K6 T8 R9 S10 R12 G13 M14 R15 R16 S17 H18 S26 S28 V29 R39 H40 Y48 R49

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0000302 response to reactive oxygen species
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0009314 response to radiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6tbv, PDBe:6tbv, PDBj:6tbv
• PDBsum: 6tbv
• PubMed: 32094585
• UniProt: P0A7N4|RL32_ECOLI Large ribosomal subunit protein bL32 (Gene Name=rpmF)