Structure of PDB 6qdw Chain t Binding Site BS01

Receptor Information

>6qdw Chain t (length=93) Species: 469008 (Escherichia coli BL21(DE3))

MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKL
FEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNL

Ligand information

>6qdw Chain b (length=2888)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacagugugac
ugcguaccuuuuguauaaugggucagcgacuuauauucuguagcaagguu
aaccgaauaggggagccgaagggaaaccgagucuuaacugggcguuaagu
ugcaggguauagacccgaaacccggugaucuagccaugggcagguugaag
guuggguaacacuaacuggaggaccgaaccgacuaauguugaaaaauuag
cggaugacuuguggcugggggugaaaggccaaucaaaccgggagauagcu
gguucuccccgaaagcuauuuagguagcgccucgugaauucaucuccggg
gguagagcacuguuucggcaagggggucaucccgacuuaccaacccgaug
caaacugcgaauaccggagaauguuaucacgggagacacacggcgggugc
uaacguccgucgugaagagggaaacaacccagaccgccagcuaagguccc
aaagucaugguuaagugggaaacgauguggaaggccagacagccaggaug
uuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacugguc
gagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaagcu
gcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagccu
gugaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcug
acauaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaag
gguuccuguccaacguuaaucggggcagggugagucgaccccuaaggcga
ggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuuggu
guuacugcgaaggggggacggagaaggcuauguuggccgggcgacgguug
ucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaa
ggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcccu
gcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccccaa
accgacacagguggucagguagagaauaccaaggcgcuugagagaacucg
ggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgcu
gauauguaggugaggucccucgcggauggagcugaaaucagucgaagaua
ccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaa
aguggacguauacggugugacgccugcccggugccggaagguuaauugau
gggguuagcggcgaagcucuugaucgaagccccgguaaacggcggccgua
acuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgacc
ugcacgaauggcguaaugauggccaggcugucuccacccgagacucagug
aaauugaacucgcugugaagaugcaguguacccgcggcaagacggaaaga
ccccgugaaccuuuacuauagcuugacacugaacauugagccuugaugug
uaggauaggugggaggcuuugaaguguggacgccagucugcauggagccg
gccuugaaauaccacccuuuaauguuugauguucuaacguuggccccuga
ucgggguugcggacagugucugguggguaguuugacuggggcggucuccu
ccuaaagaguaacggaggagcacgaagguuggcuaauccuggucggacau
caggagguuagugcaauggcauaagccagcuugacugcgagcgugacggc
gcgagcaggugcgaaagcaggucauagugauccggugguucugaauggaa
gggccaucgcucaacggauaaaagguacuccggggauaacaggcugauac
cgcccaagaguucauaucgacggcgguguuuggcaccucgaugucggcuc
aucacauccuggggcugaaguaggucccaaggguauggcuguucgccauu
uaaagugguacgcgagcuggguuuagaacgucgugagacaguucgguccc
uaucugccgugggcgcuggagaacugaggggggcugcuccuaguacgaga
ggaccggaguggacgcaucacugguguucggguugucaugccaauggcac
ugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcac
gaaacuugccccgagaugaguucucccugacuccuugagaguccugaagg
aacguugaagacgacgacguugauaggccggguguguaagcgcagcgaug
cguugagcuaaccgguacuaaugaaccgugaggcuaac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qdw Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
• Resolution: 2.83 Å
• Binding residue (original residue number in PDB): M1 R3 H15 S17 K19 T39 K40 N59 T60 L61 V62 K64 K66 H70 R73 G75 R76 R77 S78 K81 K82 Y84
• Binding residue (residue number reindexed from 1): M1 R3 H15 S17 K19 T39 K40 N59 T60 L61 V62 K64 K66 H70 R73 G75 R76 R77 S78 K81 K82 Y84

Gene Ontology

Molecular Function

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

Biological Process

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

Cellular Component

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

External links

• PDB: RCSB:6qdw, PDBe:6qdw, PDBj:6qdw
• PDBsum: 6qdw
• PubMed: 33149120
• UniProt: C6EGE8