Structure of PDB 6vyz Chain c Binding Site BS01

Receptor Information

>6vyz Chain c (length=77) Species: 562 (Escherichia coli)

SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRV
SAKGMRVIDKKGIDTVLAELRARGEKY

Ligand information

>6vyz Chain a (length=2880)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugaaaaa
uuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggagau
agcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucuc
cggggguagagcacuguuucggcaagggggucaacccgacuuaccaaccc
gaugcaaacugcgaauaccggagaauguuaucacgggagacacacggcgg
ggcuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggu
cccaaagucaugguuaagugggaaacgaugugggaaggcccagacagcca
ggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucac
uggucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccg
aagcugcggcagcgacgcuuaugcguuguuggguaggggagcguucugua
agccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaa
ugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaaga
ccaaggguuccuguccaacguuaaucggggcagggugagucgaccccuaa
ggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguac
uugguguuacugcgaaggggggacggagaaggcuauguuggccgggcgac
gguugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaa
aucaaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaau
gcccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguac
cccaaaccgacacgguggucagguagagaauaccaaggcgcuugagagaa
cucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggca
cgcugauauguaggugaggucccucgcggauggagcugaaaucagucgaa
gauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaaca
cgaaaguggacguauacggugugacgccucccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccgaacaaacgguccuaagguagcgaaauccuugucggguaaguuccga
cugcacgaauggcguaaugauggccaggcugucuccacccgagacucagu
gaaauugaacucgcugugagaugcaguguacccgcggcaagacggaaaga
ccccguaaccuuacuauagcuugacacugaacauugagccuugaugugua
ggauaggugggaggcuuugaaguguggacgccagucugcauggagccgac
cuugaaauaccacccuuuaauguuugauguucuaacguugacccguaauc
cggguugcggacagugucugguggguaguuugacugggcggucuccuccu
aaagaguaacggaggagcacgaagguuggcuaauccuggucggacaucag
gagguuagugcaauggcauaagccagcuugacugcgagcgugacggcgcg
agcaggugcgaaagcaggucauagugauccggugguucugaauggaaggg
ccaucgcucaacggauaaaagguacuccgggauaacaggcgauaccgccc
aagaguucauaucgacggcgguguuuggcacucggucggcucaucacauc
cuggggcugaaguaggucccaaggguauggcguucgccauuuaaaguggu
acgcgagcggguuuagaacgucgugagacagucggucccuaucugccgug
ggcgcuggagaacugaggggggcugcuccuaguacgagaggaccggagug
gacgcaucacugguguucggguugucaugccaauggcacugcccgguagc
uaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuugccc
cgagaugaguucucccugacccuuuaaggguccugaaggaacguugaaga
cgacgacguugauaggccggguguguaagcgcagcgaugcguugagcuaa
ccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vyz Structural basis of transcription-translation coupling.
• Resolution: 9.9 Å
• Binding residue (original residue number in PDB): S2 R3 K10 R11 V13 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 R10 V12 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:6vyz, PDBe:6vyz, PDBj:6vyz
• PDBsum: 6vyz
• PubMed: 32820061
• UniProt: P0A7M2|RL28_ECOLI Large ribosomal subunit protein bL28 (Gene Name=rpmB)