Structure of PDB 5j4d Chain LB Binding Site BS01

Receptor Information

>5j4d Chain LB (length=202) Species: 262724 (Thermus thermophilus HB27)

MYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

Ligand information

>5j4d Chain GB (length=2880)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccauc
cuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaa
ugaucggggcucaagcccagcgccgaagcugcgggucugggggaugaccc
caggcgguaggggagcguucccgaugccgaugaaggccgacccgcgaggg
cggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagag
ggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucgu
cagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaa
gggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacg
cucuaggcuagggggaccggagccauggacgagcccggccagaagcgcag
ggugggagguaggcaaauccgccucccaaaagcucugcgugguggggaag
cccguacgggugacaaccccccgaagccagggagccaagaaaagccucua
agcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggug
caagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaagu
uggccccguaacuucgggagaaggggugcucccuggggugaugagcuccg
gggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcuc
ucugcgaacucguaagaggagguauagggagcgacgcuugcccggugccg
gaaggucaaggggaggggugcaagccccgaaccgaagccccggugaacgg
cggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaag
uuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggg
acccggugaaauugaacuggccgugaagaugcggccuacccguggcagga
cgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucg
cgccugcguaggauaggugggagccugugaacccccgccuccgggugggg
gggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccuc
ggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccucc
uaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaaucc
gccggagagcgcaaggguagaagggggccugacugcgaggccugcaagcc
gagcaggggcgaaagccgggccuagugaaccgguggucccguguggaagg
gccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucucc
cccgagcguccacagcggcggggagguuuggcaccucgaugucggcucgu
cgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauua
aagcggcacgcgagcuggguucagaacgucgugagacaguucggucucua
uccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagagg
accggaagggacgcaccucugguuucccagcugucccuccaggggcauaa
gcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcggg
aagcccgccccaagaugaggccucccacggcgucaagccgguaaggaccc
gggaagacgacccgguggaugggccggggguguaagcgccgcgaggcguu
gagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5j4d Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): N29 H31 W34 E35 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 R74 H75 G76 P81 I82 F83 V84 G85 V88 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 R106 K108 K135 T136 K137 R165 R168 N169 L170 P171 L176 E179 G180 N182 Y184 R205
• Binding residue (residue number reindexed from 1): N24 H26 W29 E30 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 T46 T48 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 R69 H70 G71 P76 I77 F78 V79 G80 V83 V84 F85 P87 P89 R90 Y94 T95 P97 K98 K99 R101 K103 K130 T131 K132 R160 R163 N164 L165 P166 L171 E174 G175 N177 Y179 R200

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5j4d, PDBe:5j4d, PDBj:5j4d
• PDBsum: 5j4d
• PubMed: 27107638
• UniProt: Q72I05|RL4_THET2 Large ribosomal subunit protein uL4 (Gene Name=rplD)