Structure of PDB 6ys3 Chain f Binding Site BS02

Receptor Information

>6ys3 Chain f (length=177) Species: 469008 (Escherichia coli BL21(DE3))

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFR

Ligand information

>6ys3 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: 6ys3 Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM peptide
• Resolution: 2.58 Å
• Binding residue (original residue number in PDB): K33 T35 N37 M38 G39 G41 T68 A70 R71 K72 F77 I85 K88 S121 F122 D123 R125 S129 G131 R150 G151 L152 D153 T155
• Binding residue (residue number reindexed from 1): K32 T34 N36 M37 G38 G40 T67 A69 R70 K71 F76 I84 K87 S120 F121 D122 R124 S128 G130 R149 G150 L151 D152 T154

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

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

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ys3, PDBe:6ys3, PDBj:6ys3
• PDBsum: 6ys3
• UniProt: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)