Structure of PDB 8bim Chain A Binding Site BS01

Receptor Information

>8bim Chain A (length=271) Species: 83333 (Escherichia coli K-12)

AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS

Ligand information

>8bim Chain 0 (length=2758)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggcuuaccaacccgaugca
aacugcgaauaccggagaauguuaucacgggagacacacggcgggugcua
acguccgucgugaagagggaaacaacccagaccgccagcuaaggucccaa
agucaugguuaagugggaaacgaugugggaaggcccagacagccgagucg
gccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggca
gcgacgcuuaugcguuguuggguaggggagcguucuguaagccugcgaag
gugugcugugaggcaugcuggagguaucagaagugcgaaugcugacauaa
guaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguucc
uguccaacguuaaucggggcagggugagucgaccccuaaggcgaggccga
aaggcguagucgaugggaaacagguuaauauuccuguacuugguguuacu
gcgaaggggggacggagaaggcuauguuggccgggcgacgguugucccgg
uuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcuga
ggcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcuucc
aggaaaagccucuaagcaucagguaacaucaaaucguaccccaaaccgac
acagguggucagguagagaauaccaaggcgcuugagagaacucgggugaa
ggaacuaggcaaaauggugccguaacuucgggagaaggcacgcugauaug
uaggugaggucccucgcggauggagcugaaaucagucgaagauaccagcu
ggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaagugga
cguauacggugugacgccugcccggugccggaagguuaauugaugggguu
agcgcaagcgaagcucuugaucgaagccccgguaaacggcggccguaacu
auaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccugc
acgaauggcguaaugauggccaggcugucuccacccgagacucagugaaa
uugaacucgcugugaagaugcaguguacccgcggcaagacggaaagaccc
cgugaaccuuuacuauagcuugacacugaacauugagccuguuugauguu
cuaacguugacccguaauccggguugcggacagugucugguggguaguuu
gacuggggcggucuccuccuaaagaguaacggaggagcacgaagguuggc
uaauccuggucggacaucaggagguuagugcaauggcauaagccagcuug
acugcgagcgugacggcgcgagcaggugcgaaagcaggucauagugaucc
ggugguucugaauggaagggccaucgcucaacggauaaaagguacuccgg
ggauaacaggcugauaccgcccaagaguucauaucgacggcgguguuugg
caccucgaugucggcucaucacauccuggggcugaaguaggucccaaggg
uauggcuguucgccauuuaaagugguacgcgagcuggguuuagaacgucg
ugagacaguucggucccuaucugccgugggcgcuggagaacugagggggg
cugcuccuaguacgagaggaccggaguggacgcaucacugguguucgggu
ugucaugccaauggcacugcccgguagcuaaaugcggaagagauaagugc
ugaaagcaucuaagcacgaaacuugccccgagaugaguucucccugaccc
uuuaaggguccugaaggaacguugaagacgacgacguugauaggccgggu
guguaagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugagg
cuuaaccu

<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<<..>>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<<<..>>.>>...>>>>.>>>
..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<....
..>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((..
...<<<<<<...........<<..<<<<<..<<..............>>.
.>>>>>.>>...........))).....>>>>>>.>>>...>>>>>>><<
<<<<<<<....>>>>>>>>>....>>>>>><<<<<<<...<<<......<
<<<<<<<....>>>>>>>>...>>>..>>>>>.>>.....>>>>>><...
...<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<
<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<...<<<..
..>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<
<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>
><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>..
.>>>>...>><..<<<<<<..>>>>>>...>>>>>>...>>>...>>>.>
........>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<
<.........<.....<<<<<.....<..>......>>>>><<<<<<...
..<<<...<<<<.....>>>>...>>>...>>>>>>............<<
<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>..
.....>>>>>>>.<<<<<.<<<..<<<<<<<..<<<<.......<<<<<<
.<<....>>..>>>>>>.......>>>>>>>>>..>>>>><<<<<<....
...>>>>>>........<...........<<<<<.......>>>>>....
.>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>....
.>.....<<<<<........>>>>>..<<<<<<<<.(((.[[......<<
<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<..>>>>>>>>>>
>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..
<<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<
...<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>..
.<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>))).......<
<<<<<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>
>.......<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>>
>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>
.<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<.
...>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..
<<<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<
<<<<<.)))..>>>>>..>>>>>...>>>>.>>>>>...<<<.<..<<<<
<...........>>>>>...>>>>.>>>>.......>>>>>>>..<<<<<
.....>>>>><....<<..<<<<<.......>>>>>....<<<<<<<<..
<<....<<<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>
>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bim Modulation of translational decoding by m 6 A modification of mRNA.
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): K7 P8 G12 R13 R14 H15 K18 K36 R43 N44 N45 N46 R48 T50 R52 H53 G56 H58 K59 Y62 R63 I74 Y83 D98 E100 R101 K147 K150 Q153 L154 A155 R156 S157 A158 L176 R177 S178 E180 R182 H200 M201 L205 G206 K207 A208 R212 W213 R217 T219 V220 R221 T223 M225 N226 D229 H232 G235 E236 R238 G241 H243 P247 K253 G254 K255 T257 R258 R262 K265 R270 R271
• Binding residue (residue number reindexed from 1): K6 P7 G11 R12 R13 H14 K17 K35 R42 N43 N44 N45 R47 T49 R51 H52 G55 H57 K58 Y61 R62 I73 Y82 D97 E99 R100 K146 K149 Q152 L153 A154 R155 S156 A157 L175 R176 S177 E179 R181 H199 M200 L204 G205 K206 A207 R211 W212 R216 T218 V219 R220 T222 M224 N225 D228 H231 G234 E235 R237 G240 H242 P246 K252 G253 K254 T256 R257 R261 K264 R269 R270

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0032297 negative regulation of DNA-templated DNA replication initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990082 DnaA-L2 complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8bim, PDBe:8bim, PDBj:8bim
• PDBsum: 8bim
• PubMed: 37553384
• UniProt: P60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)