Structure of PDB 6qdw Chain 6 Binding Site BS01

Receptor Information

>6qdw Chain 6 (length=46) Species: 469008 (Escherichia coli BL21(DE3))

MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

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 T4 F5 Q6 P7 S8 V9 L10 K11 R12 N13 R14 S15 H16 G17 F18 R19 R21 K25 N26 Q29 R33 R34 R35 K37 G38 R39 A40 S45
• Binding residue (residue number reindexed from 1): M1 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 N13 R14 S15 H16 G17 F18 R19 R21 K25 N26 Q29 R33 R34 R35 K37 G38 R39 A40 S45

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• 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: P0A7P5|RL34_ECOLI Large ribosomal subunit protein bL34 (Gene Name=rpmH)