Structure of PDB 6ztm Chain BY Binding Site BS01

Receptor Information

>6ztm Chain BY (length=77) Species: 562 (Escherichia coli)

SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRV
SAKGMRVIDKKGIDTVLAELRARGEKY

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): S2 R3 K10 T14 G15 N16 R18 S19 A21 L22 N23 K26 R27 R28 F29 L30 P31 N32 H34 H36 R37 R50 A53 K54 M56 R57 K61 K62
• Binding residue (residue number reindexed from 1): S1 R2 K9 T13 G14 N15 R17 S18 A20 L21 N22 K25 R26 R27 F28 L29 P30 N31 H33 H35 R36 R49 A52 K53 M55 R56 K60 K61

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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: P0A7M2|RL28_ECOLI Large ribosomal subunit protein bL28 (Gene Name=rpmB)