Structure of PDB 8b0x Chain y Binding Site BS01

Receptor Information

>8b0x Chain y (length=58) Species: 37762 (Escherichia coli B)

AKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAV
SFMVKVEE

Ligand information

>8b0x Chain a (length=2748)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacagcugugu
gacugcguaccuuuuguauaaugggucagcgacuuauauucuguagcaag
guuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcguua
aguugcaggguauagacccgaaacccggugaucuagccaugggcagguug
aagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaaaau
uagcggaugacuuguggcugggggugaaaggccaaucaaaccgggagaua
gcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucucc
ggggguagagcacuguuucggcaagggggucaucccgacuuaccaacccg
augcaaacugcgaauaccggagaauguuaucacgggagacacacggcggg
ugcuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggu
cccaaagucaugguuaagugggaaacgaugugggaaggcccagacagcgu
cgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaagc
ugcggcagcgacgcgcguuguuggguaggggagcguucuguaagccugug
aaggugugcugugaggcaugcuggagguaucagaagugcgaaugcugaca
uaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaagggu
uccuguccaacguuaaucggggcagggugagucgaccccuaaggcgaggc
cgaaaggcguagucgaugggaaacagguuaauauuccuguacuugguguu
acugcgaaggggggacggagaaggcuauguuggccgggcgacgguugucc
cgguuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggc
ugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcu
uccaggaaaagccucuaagcaucagguaacaucaaaucguaccccaaacc
gacacagguggucagguagagaauaccaaggcgcuugagagaacucgggu
gaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgcugau
auguaggugaggucccucgcggauggagcugaaaucagucgaagauacca
gcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaagu
ggacguauacggugugacgccugcccggugccggaagguuaauugauggg
guuagcggcgcgaagcucuugaucgaagccccgguaaacggcggccguaa
cuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccu
gcacgaauggcguaaugauggccaggcugucuccacccgagacucaguga
aauugaacucgcugugaagaugcaguguacccgcggcaagacggaaagac
cccgugaaccuuuacuauagcuugacacugaacauauguucuaacguugg
ccccugaucgggguugcggacagugucugguggguaguuugacuggggcg
gucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggu
cggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcg
ugacggcgcgagcaggugcgaaagcaggucauagugauccggugguucug
aauggaagggccaucgcucaacggauaaaagguacuccggggauaacagg
cugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgaug
ucggcucaucacauccuggggcugaaguaggucccaaggguauggcuguu
cgccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguu
cggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuag
uacgagaggaccggaguggacgcaucacugguguucggguugucaugcca
auggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcauc
uaagcacgaaacuugccccgagaugaguucucccugacuccuugagaguc
cugaaggaacguugaagacgacgacguugauaggccggguguguaagcgc
agcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8b0x The translating bacterial ribosome at 1.55 angstrom resolution generated by cryo-EM imaging services.
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): S12 I14 G15 P18 K19 A22 T23 L25 G26 G28 R30 I32 R38 A43 G46 M47
• Binding residue (residue number reindexed from 1): S11 I13 G14 P17 K18 A21 T22 L24 G25 G27 R29 I31 R37 A42 G45 M46

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

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

Cellular Component

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

External links

• PDB: RCSB:8b0x, PDBe:8b0x, PDBj:8b0x
• PDBsum: 8b0x
• PubMed: 36841832
• UniProt: P0AG51|RL30_ECOLI Large ribosomal subunit protein uL30 (Gene Name=rpmD)