Structure of PDB 6ztm Chain BF Binding Site BS02

Receptor Information

>6ztm Chain BF (length=178) Species: 562 (Escherichia coli)

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFRK

Ligand information

>6ztm Chain BA (length=2901)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacagaucugu
gugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagca
agguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcgu
uaaguugcaggguauagacccgaaacccggugaucuagccaugggcaggu
ugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaaa
auuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggaga
uagcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucu
ccggggguagagcacuguuucggcaagggggucaucccgacuuaccaacc
cgaugcaaacugcgaauaccggagaauguuaucacgggagacacacggcg
ggugcuaacguccgucgugaagagggaaacaacccagaccgccagcuaag
gucccaaagucaugguuaagugggaaacgaugugggaaggcccagacagc
caggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagcuc
acuggucgagucggccugcgcggaagauguaacggggcuaaaccaugcac
cgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguucug
uaagccugugaaggugugcugugaggcaugcuggagguaucagaagugcg
aaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaa
gaccaaggguuccuguccaacguuaaucggggcagggugagucgaccccu
aaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccugu
acuugguguuacugcgaaggggggacggagaaggcuauguuggccgggcg
acgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccgga
aaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaacaa
augcccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucgu
accccaaaccgacacagguggucagguagagaauaccaaggcgcuugaga
gaacucgggugaaggaacuaggcaaaauggugccguaacuucgggagaag
gcacgcugauauguaggugaggucccucgcggauggagcugaaaucaguc
gaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaa
acacgaaaguggacguauacggugugacgccugcccggugccggaagguu
aauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaauggcguaaugauggccaggcugucuccacccg
agacucagugaaauugaacucgcugugaagaugcaguguacccgcggcaa
gacggaaagaccccgugaaccuuuacuauagcuugacacugaacauugag
ccuugauguguaggauaggugggaggcuuugaaguguggacgccagucug
cauggagccgaccuugaaauaccacccuuuaauguuugauguucuaacgu
ugacccgugauccggguugcggacagugucugguggguaguuugacuggg
gcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccu
ggucggacaucaggagguuagugcaauggcauaagccagcuugacugcga
gcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugguu
cugaauggaagggccaucgcucaacggauaaaagguacuccggggauaac
aggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccucg
augucggcucaucacauccuggggcugaaguaggucccaaggguauggcu
guucgccauuuaaagugguacgcgagcuggguuuagaacgucgugagaca
guucggucccuaucugccgugggcgcuggagaacugaggggggcugcucc
uaguacgagaggaccggaguggacgcaucacugguguucggguugucaug
ccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaagc
aucuaagcacgaaacuugccccgagaugaguucucccugacuccuugaga
guccugaaggaacguugaagacgacgacguugauaggccggguguguaag
cgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaacc
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ztm Structural basis of transcription-translation coupling and collision in bacteria.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): N37 M38 G39 V40 T68 A70 R71 F77 I79 I85 K88 S121 R125 N127 M130 G151 L152 T157
• Binding residue (residue number reindexed from 1): N36 M37 G38 V39 T67 A69 R70 F76 I78 I84 K87 S120 R124 N126 M129 G150 L151 T156

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6ztm, PDBe:6ztm, PDBj:6ztm
• PDBsum: 6ztm
• PubMed: 32820062
• UniProt: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)