Structure of PDB 7ode Chain L Binding Site BS01

Receptor Information

>7ode Chain L (length=183) Species: 83333 (Escherichia coli K-12)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFKVFKGKKMAGQMGNERVTVQSLD
VVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA

Ligand information

>7ode Chain I (length=1990)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaucuaa
guaccccgaggaaaagaaaucaaccgagauucccccaguagcggagcgaa
cggggagcagcccagagccugaaucaguguguguguuaguggaagcgucu
ggaaaggcgcgcgauacagggugacagccccguacacaaaaaugcacaug
cugugagcucgaugaguagggcgggacauccugucugaauagggggccau
ccuccaaggcuaaauacuccugacugaccgauagugaaccaguaccguga
gggaaaggcgaaaagaaccccggcgaggggagugaaaaagaaccugaaac
cguguacguacaagcagugggagcacgcaggcgugugacugcguaccuuu
uguauaaugggucagcgacuuauauucuguagcaagguuaaccgaauagg
ggagccgaaguugcaggguauagacccgaaacccggugaucuagccaugg
gcagguugaagguuggguaacacuaacuggaggaccgaaccgacuaaugu
ugaaaaauuagcggaugacuuguggcugggggugaaaggccaaucaaacc
gggagauagugguucuccccgaaagcuaguagcgccucgugaauucaucu
ccgcggagaauguuaucacgggagacacacggcgggugcaaguccgucgu
gaagagggaaacaacccagaccgccagcuaaggucccaaagucaugguua
agugggauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgc
gcguuguuggguaggggagcguucuguaagccugcgaaggugugcuguga
ggcaugcuggagguaucagaagugcgaaugcugacauaaguaacgauaaa
gcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaacguu
aaucggggcagggugagucgaccccuaaggcgaggccgaaaggcguaguc
gaugggaaacagguuaauauuccuguacuugguguuacugcgaagggggg
acggagaaggcuauguuggccgggcgacgguugucccgguuuaagcgugu
aggcugguuuuccaggcaaauccggaaaaucaaggcugaggcgugaugac
gaggcacuggugcugaagcaacaaaugcccugcuuccaggaaaagccucu
aagcacagguaacaucaaaucguaccccaaaccgacacagguggucaggu
agagaauaccaaggcgcuugagagaacucgggugaaggaacuaggcaaaa
uggugccguaacuucgggagaaggcacgcugauauguaggugaggucccc
gcggauggagcugaaaucagucgaagauaccagcuggcugcaacuguuua
uuaaaaacacagcacugugcaaacacgaaaguggacguauacggugugac
gccuuggcguaaugauggccaggcugucuccacccgagacucagugaaau
ugaacucgcugugaugcaguguacccgcggcaagaggaguugacccguau
ccggguugcucccuaucugccgugggcgcuggagaacugaggggggcugc
uccuaguacgagaggaccggaguggacgcaucacugguguucggguuguc
augccaauggcacugcccgguagcuaaaugcggaagagauaagugcgcac
gaacuugccccgagaugaguucucccugacccuuuaaggguccugaagga
acguugaagacgacgacguugauaggccggguguguaagcgcagcgaugc
guugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ode Structural Consequences of Deproteinating the 50S Ribosome.
• Resolution: 2.84 Å
• Binding residue (original residue number in PDB): M11 T12 P23 Q36 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 G120 R124 K154 V155 K157 K159 M161 A162 Q164 R169 V170 T171 Q173 S174 A192 V193 P194 A196 T197 K208
• Binding residue (residue number reindexed from 1): M11 T12 P23 Q36 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 G120 R124 K128 V129 K131 K133 M135 A136 Q138 R143 V144 T145 Q147 S148 A166 V167 P168 A170 T171 K182

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:7ode, PDBe:7ode, PDBj:7ode
• PDBsum: 7ode
• PubMed: 36358955
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)