Structure of PDB 9cl9 Chain D Binding Site BS01

Receptor Information

>9cl9 Chain D (length=157) Species: 83333 (Escherichia coli K-12)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLI
VKPAVKA

Ligand information

>9cl9 Chain CA (length=1543)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaccgagauucccccaguagcggcgagcgaacgg
ggagcagcccagagccugaaucaguguguguguuaguggaagcgucugga
aaggcgcgcgauacagggugacagccccguacacaaaaaugcacaugcug
ugagcucgaugaguagggcgggacacgugguauccugucugaauaugggg
ggaccauccuccaaggcuaaauacuccugacugaccgauagugaaccagu
accgugagggaaaggcgaaaagaaccccggcgaggggagugaaaaagaac
cugaaaccguguacguacaagcagugggagcacgcuuaggcgugugacug
cguaccuuuuguauaaugggucagcgacuuauauucuguagcaagguuaa
ccgaauaggggagccgaagggaaaaguugcaggguauagacccgaaaccc
ggugaucuagccaugggcgacuuguggcuggucaaaccgggagauagcug
guucuccccgaaagcuauuuagguagcgccucgugaauucguuaucacgg
gagacacacggcggggcuaacguccgucgugaagagggaaacaacccaga
ccgccagcuaaggucccaaagucaugguuaagugggaaacgagcggaaga
uguaacggggcuaaaccaugcaccgaagcugcggcagcgacgcuuaugcg
uuguuggguaggggagcguucuguaagccugcgaaggugugcugugaggc
augcuggagguaucagaagugcgaaugcugacauaaguaacgauaaagcg
ggugaaaagcccgcucgccggaagaccaaggguuccuguccaacguuaau
cggggcagggugagucgaccccuaaggcgaggcguagucgaugggaaaca
gguuaauauuccuguacuugguguuacugguaacaucaaaucguacccca
aaccgacacgguggucagguagagaauaccaaggcgcuugagagaacucg
cgagacucagugaaauugaacucgcugugagaugcaguguacccgcggcu
ggcuguucgccaugaacgucgugagacaguucgccgugggcgcuggagaa
cugaggggggcugcuccuaguacgagaggaccggaguggacgcaucacug
guguucggguugucaugccaauggcacugcccgguagcuaaaugcggaag
agauaagugccacgaaacuugccccgagaugaguucucccugacccuuua
aggguccugaaggaacguugaagacgacgacguugauaggccgggugugu
aaguugagcuaaccgguacuaaugaaccgugaggcuuaaccuu

<<<<<.<<......<<<<<<<<<<<......<...<.<<....<<.....
.......<<.....((.>>......<<<<.....<<<)).....>>>...
......>>>>..........<........>.<<............>>...
..<<<<<<.........>>>>>>............<<<<...........
.......>>>>.................<<..................>>
.......<<....<........<.......<<<...<<.......<....
...>...(........<<......).>>...>>.....>>>.......>.
.....>..........<......................>......<<<.
.........>>>..>>.......>>.....>>..>..............<
.<.......>..>>..........<.<........>>.............
.....>>>>>>>>>>>..........<....................>..
.....<...........>.<<<<<<.....<<..<.<.........<...
............>..................>.>.>>...........<<
.........<<<.<<.<....>>>.>>>...........>>.........
......<<<.........<...>.......<<<<<<........>>>>>>
............<<<.......>>>..........<<........>>...
.<<<.<<<......<<..........((......................
.......>>.....))...........>>>>>>...<..<..........
.>..>......>>>...<.<<<.....<<........<<<<<<....>>>
>>>.....>>....>>>..>......>>>>>>................<<
<.........>>>................<<...<<<<<<..........
...>>>>>>......<<.....<....<........>.....>.......
<<.........>>......<<<<<<<<<>>>>>>>>>....>>..>>...
..................<<<.....>>>............<.....<<.
.>>...>...............<<.<..........>>>.....<<....
..................<<....>>.........>>............<
...........<<<<..<..............>.>>>>...<.<......
<.....<.....<<<......>>>.......>......>...>.>.....
.<....<<<.>>>.....>...............>......<<.<<<...
.>>>>>................................<<.<<<..<...
.........>..>>>...>>.............>.>>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9cl9 50S ribosome assembly intermediates at low temperature reveal bound RluB
• Resolution: 5.04 Å
• Binding residue (original residue number in PDB): N42 K56 N58 P63 G66 H67 R169 S174 G191 A192
• Binding residue (residue number reindexed from 1): N42 K56 N58 P63 G66 H67 R117 S122 G139 A140

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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:9cl9, PDBe:9cl9, PDBj:9cl9
• PDBsum: 9cl9
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)