Structure of PDB 4wsd Chain 31 Binding Site BS01

Receptor Information

>4wsd Chain 31 (length=202) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

Ligand information

>4wsd Chain 1H (length=2912)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccga
aaaguccgcggccguggacccgaaaccgggcgagcuagcccuggccaggg
ugaagcuggggugagacccaguggaggcccgaaccggugggggaugcaaa
ccccucggaugagcuggggcuaggagugaaaagcuaaccgagcccggaga
uagcugguucuccccgaaaugacuuuagggucagccucaggcgcugacug
gggccuguagagcacugauagggcuagggggcccaccagccuaccaaacc
cugucaaacuccgaagggucccagguggagccugggagugagggcgcgag
cgauaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaagg
cccccaagucugggcuaagugguaaaggauguggcgccgcgaagacagcc
aggauguuggcuuagaagcagccaucauuuaaagagugcguaauagcuca
cuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgcc
gaagcugcgggucugggggaugaccccaggcgguaggggagcguucccga
ugccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcga
augccggcaugaguaacgauaaagagggugagaaucccucucgccguaag
cccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccua
aggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcc
cuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagcc
auggacgagcccggccagaagcgcagggugggagguaggcaaauccgccu
cccaacaagcucugcgugguggggaagcccguacgggugacaaccccccg
aagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgua
ccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggga
gaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaag
gggugcucccuggggugaugagccccggggagccgcagugaacaggcucu
ggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggu
auagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaa
gccccgaaccgaagccccggugaacggcggccguaacuauaacgguccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgua
acgaccggagcgcugucucggcgagggacccggugaaauugaacuggccg
ugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuua
cugcagccugguguuggcucuuggucgcgccugcguaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaaauaccac
ccuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaa
agguccccucaggcgggacggaaauccgccggagagcgcaaggguagaag
ggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccu
agugaaccgguggucccguguggaagggccaucgaucaacggauaaaagu
uaccccggggauaacaggcugaucucccccgagcguccacagcggcgggg
agguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggu
cccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguuca
gaacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuu
gaggggggcucuuccuaguacgagaggaccggaagggacgcaccucuggu
uucccagcugucccuccaggggcauaagcuggguagccaugugcggaagg
gauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccu
cccacggcgucaagccgguaaggacccgggaagaccacccgguggauggg
ccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgucc
gaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wsd Structural insights into the translational infidelity mechanism.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): N29 H31 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 K52 R54 G55 V57 A58 Y59 S60 G61 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 P81 I82 F83 V84 G85 V88 V89 F90 P92 R95 Y99 T100 P102 K103 K104 R106 K108 K135 T136 K137 R165 R168 N169 P171 T175 G180 Y184 R205
• Binding residue (residue number reindexed from 1): N24 H26 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 T46 K47 R49 G50 V52 A53 Y54 S55 G56 K58 Q62 K63 H64 G66 R67 A68 R69 H70 G71 P76 I77 F78 V79 G80 V83 V84 F85 P87 R90 Y94 T95 P97 K98 K99 R101 K103 K130 T131 K132 R160 R163 N164 P166 T170 G175 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:4wsd, PDBe:4wsd, PDBj:4wsd
• PDBsum: 4wsd
• PubMed: 26037619
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)