Structure of PDB 8qbt Chain D Binding Site BS01

Receptor Information

>8qbt Chain D (length=209) Species: 679895 (Escherichia coli BW25113)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

Ligand information

>8qbt Chain A (length=2841)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagucgag
ucggccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcg
gcagcgacgcuuaugcguuguuggguaggggagcguucuguaagccugcg
aaggugugcugugaggcaugcuggagguaucagaagugcgaaugcugaca
uaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaagggu
uccuguccaacguuaaucggggcagggugagucgaccccuaaggcgaggc
cgaaaggcguagucgaugggaaacagguuaauauuccuguacuugguguu
acugcgaaggggggacggagaaggcuauguuggccgggcgacgguugucc
cgguuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggc
ugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcu
uccaggaaaagccucuaagcaucagguaacaucaaaucguaccccaaacc
gacacagguggucagguagagaauaccaaggcgcuugagagaacucgggu
gaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgcugau
auguaggugaggucccucgcggauggagcugaaaucagucgaagauacca
gcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaagu
ggacguauacggugugacgccugcccggugccggaagguuaauugauggg
guuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggccgua
acuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgacc
ugcacgaauggcguaaugauggccaggcugucuccacccgagacucagug
aaauugaacucgcugugaagaugcaguguacccgcggcaagacggaaaga
ccccgugaaccuuuacuauagcuugacacugaacauugagccuugaugug
uaggauaggugggaggcuuugaaguguggacgccagucugcauggagccg
accuugaaauaccacccuuuaauguuugauguucuaacguugaccccuaa
ucgggguugcggacagugucugguggguaguuugacuggggcggucuccu
ccuaaagaguaacggaggagcacgaagguuggcuaauccuggucggacau
caggagguuagugcaauggcauaagccagcuugacugcgagcgugacggc
gcgagcaggugcgaaagcaggucauagugauccggugguucugaauggaa
gggccaucgcucaacggauaaaagguacuccggggauaacaggcugauac
cgcccaagaguucauaucgacggcgguguuuggcaccucgaugucggcuc
aucacauccuggggcugaaguaggucccaaggguauggcuguucgccauu
uaaagugguacgcgagcuggguuuagaacgucgugagacaguucgguccc
uaucugccgugggcgcuggagaacugaggggggcugcuccuaguacgaga
ggaccggaguggacgcaucacugguguucggguugucaugccaauggcac
ugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcac
gaaacuugccccgagaugaguucucccugacccuuuaaggguccugaagg
aacguugaagacgacgacguugauaggccggguguguaagcgcagcgaug
cguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qbt Novel arrest peptides induce ribosome stalling by short circuiting the ribosomal peptidyltransferase activity
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): M11 R13 P23 Q36 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 G120 K123 R124 F127 R128 T129 Q130 A132 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 L175 K190 A192 V193 P194 G195 A196 T197 K208
• Binding residue (residue number reindexed from 1): M11 R13 P23 Q36 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 G120 K123 R124 F127 R128 T129 Q130 A132 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 L175 K190 A192 V193 P194 G195 A196 T197 K208

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8qbt, PDBe:8qbt, PDBj:8qbt
• PDBsum: 8qbt
• PubMed: 38503735
• UniProt: C3SQU2