Structure of PDB 3j3w Chain 5 Binding Site BS01

Receptor Information

>3j3w Chain 5 (length=120) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

AKKGKKYVEAAKLVDRSKAYDVSEAVALVKKTNTAKFDATVEVAFRLGVD
PRKNDQQDKAGNIHVPIGKVSFEDEKLVENFTTMYDTILKAKPAAAKGVY
VKNVAVTSTMGPGVKVDSST

Ligand information

>3j3w Chain A (length=2685)

gguuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgau
gaaggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuu
gauccggagauuuccgaauggggaaacccaccacucguaauggaguggua
uccauaucugaauucauaggauaugagaaggcagacccggggaacugaaa
caucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcg
gcgagcgaaacgggauuagcccaaaccaagaggcuugccucuugggguug
uaggacacucuguacggaguuacaaaggaacgagguagaugaagaggucu
ggaaaggcccgccauaggagguaacagcccuguagucaaaacuucguucu
cuccugaguggauccugaguacggcggaacacgugaaauuccgucggaau
ccgggaggaccaucucccaaggcuaaauacucccuagugaccgauaguga
accaguaccgugagggaaaggugaaaagcaccccggaaggggagugaaag
agauccugaaaccgugugccuacaaguagucagagcccguuaacggguga
uggcgugccuuuuguagaaugaaccggcgaguuacgaucccgugcaaggu
uaagcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcau
gaguacguggucguagacccgaaaccaggugaucuacccauguccagggu
gaaguucagguaacacugaauggaggcccgaacccacgcacguugaaaag
ugcggggaugagguguggguaggggugaaaugccaaucgaaccuggagau
agcugguucucuccgaaauagcuuuagggcuagccucaagguaagagucu
uggagguagagcacugauuggacuaggggccccuaccggguuaccgaauu
cagucaaacuccgaaugccaaugacuuauccuugggagucagacugcgag
ugauaagauccguagucgaaagggaaacagcccagaccgccagcuaaggu
cccaaaguauacguuaaguggaaaaggauguggaguugcuuagacaacca
ggauguuggcuuagaagcagccaccauuuaaagagugcguaauagcucac
uggucgagugacucugcgccgaaaauguaccggggcuaaacguaucaccg
aagcugcggacuguucuucgaacagugguaggagagcguucuaagggcug
ugaagccagaccggaaggacugguggagcgcuuagaagugagaaugccgg
uaugaguagcgaaagaggggugagaauccccuccaccgaaugccuaaggu
uuccugaggaaggcucguccgcucaggguuagucgggaccuaagccgagg
ccgaaaggcguaggcgauggacaacagguugauauuccuguaccaccucc
ucaccauuugagcaauggggggacgcaggaggauaggguaagcgcgguau
uggauauccgcguccaagcaguuaggcugggaaauaggcaaauccguuuc
ccauaaggcugagcugugauggcgagcgaaauauaguagcgaaguuccug
auuccacacugccaagaaaagccucuagcgaggugagaggugcccguacc
gcaaaccgacacagguaggcgaggagagaauccuaaggugaucgagagaa
cucucguuaaggaacucggcaaaaugaccccguaacuucgggagaagggg
ugcucuguuagggugcaagcccgagagagccgcagugaauaggcccaggc
gacuguuuagcaaaaacacaggucucugcgaagccguaaggcgaaguaua
ggggcugacgccugcgcggccguaacuauaacgguccuaagguagcgaaa
ggcgcaacgaucugggcacugucucaacgagagacucggugaaauuauag
uaccugugaagaugcagguuacccgcgacaggacggaaagaccccgugga
gcuuuacugcagccugauauugaauguugguacagcuuguacaggauagg
uaggagccuuggaaaccggagcgccagcuucgguggaggcaucgguggga
uacuacccuggcuguauugaccuucuaacccgccgcccuuaucgggcggg
gagacagugucaggugggcaguuuggugauccggugguuccgcauggaag
ggccaucgcucaacggauaaaagcuaccccggggauaacaggcuuaucuc
ccccaagaguccacaucgacggggagguuuggcaccucgaugucggcuca
ucgcauccuggggcuguagucagucccaaggguugggcuguucgcccauu
aaagcgguacgcgagcuggguucagaacgucgugagacaguucggucccu
auccgucgcgggcgcaggaaauuugagaggagcuguccuuaguacgagag
gaccgggauggacgcaccgcugguguaccaguuguucugccaagggcauc
gcuggguagcuaugugcggacgggauaagugcugaaagcaucuaagcaug
aagccccccucaagaugagauuucccauuccgcaaggaaguaagaucccu
gaaagaugaucagguugauaggucugagguggaaguguggcgacacaugg
agcugacagauacuaaucgaucgaggacuuaacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j3w Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit
• Resolution: 10.7 Å
• Binding residue (original residue number in PDB): A2 K3 K4 G5 K7 Y8 A11 A12 R17 N34 T35 A36 A40 T41 E43 V44 F46 R47 D51 P52 R53 K54 N55 D56 Q58 D166 K167 A168 N170 I171 H172 P174 K205 T215 T217 M218
• Binding residue (residue number reindexed from 1): A1 K2 K3 G4 K6 Y7 A10 A11 R16 N33 T34 A35 A39 T40 E42 V43 F45 R46 D50 P51 R52 K53 N54 D55 Q57 D58 K59 A60 N62 I63 H64 P66 K97 T107 T109 M110

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0006417 regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:3j3w, PDBe:3j3w, PDBj:3j3w
• PDBsum: 3j3w
• PubMed: 23700310
• UniProt: Q06797|RL1_BACSU Large ribosomal subunit protein uL1 (Gene Name=rplA)