Structure of PDB 6qdw Chain 7 Binding Site BS01

Receptor Information

>6qdw Chain 7 (length=64) Species: 469008 (Escherichia coli BL21(DE3))

PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVS
KGDLGLVIACLPYA

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): P2 K3 I4 K5 T6 R8 K12 R13 T17 G18 K19 K23 H26 A27 N28 R30 H31 I32 L33 T34 K35 T38 K39 R40 K41 R42 H43 R45 K47 M49 S51 G53 D54 Y64
• Binding residue (residue number reindexed from 1): P1 K2 I3 K4 T5 R7 K11 R12 T16 G17 K18 K22 H25 A26 N27 R29 H30 I31 L32 T33 K34 T37 K38 R39 K40 R41 H42 R44 K46 M48 S50 G52 D53 Y63

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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: P0A7Q1|RL35_ECOLI Large ribosomal subunit protein bL35 (Gene Name=rpmI)