Structure of PDB 4wzd Chain B5 Binding Site BS01

Receptor Information

>4wzd Chain B5 (length=93) Species: 300852 (Thermus thermophilus HB8)

KTAYDVILAPVLSEKAYAGFAEGKYTFWVHPKATKTEIKNAVETAFKVKV
VKVNTLHVRGKKKRLGRYLGKRPDRKKAIVQVAPGQKIEALEG

Ligand information

>4wzd Chain 14 (length=2909)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuugcgcggggggaaccuggggaacugaaacaucucaguacccaga
ggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggac
cagccuaaaccguccggcuuguccgggcggggucguggggcccucggaca
ccgaauccccagccuagccgaagcuguugggaagcagcgccagagagggu
gaaagccccguaggcgaaagguggggggauaggugaggguacccgaguac
cccgugguucguggagccaugggggaaucugggcggaccaccgccuaagg
cuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuac
aagcagucacggccccgcaagggguuguggcgugccuauugaagcaugag
ccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcgua
gggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaa
guccgcggccguggacccgaaaccgggcgagcuagcccuggccaggguga
agcuggggugagacccaguggaggcccgaaccggugggggaugcaaaccc
cucggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauag
cugguucuccccgaaaugacuuuagggucagccucaggcgcugacugggg
ccuguagagcacugauagggcuagggggcccaccagccuaccaaacccug
ucaaacuccgaagggucccagguggagccugggagugagggcgcgagcga
uaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccc
ccaagucugggcuaagugguaaaggauguggcgccgcgaagacagccagg
auguuggcuuagaagcagccaucauuuaaagagugcguaauagcucacug
gucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaa
gcugcgggucugggggaugaccccaggcgguaggggagcguucccgaugc
cgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaug
ccggcaugaguaacgauaaagagggugagaaucccucucgccguaagccc
aaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagg
ugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccuu
cccgcaggugcgauggggggacgcucuaggcuagggggaccggagccaug
gacgagcccggccagaagcgcagggugggagguaggcaaauccgccuccc
aacaagcucugcgugguggggaagcccguacgggugacaaccccccgaag
ccagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccg
caaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaa
cccucgccaaggaacucugcaaguuggccccguaacuucgggagaagggg
ugcucccuggggugaugagccccggggagccgcagugaacaggcucuggc
gacuguuuaccaaaaacacagcucucugcgaacucguaagaggagguaua
gggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcc
ccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaagg
uagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacg
accggagcgcugucucggcgagggacccggugaaauugaacuggccguga
agaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacug
cagccugguguuggcucuuggucgcgccugcguaggauaggugggagccu
gugaacccccgccuccgggugggggggaggcgccggugaaauaccacccu
ggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgggc
aguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagg
uccccucaggcgggacggaaauccgccggagagcgcaaggguagaagggg
gccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagu
gaaccgguggucccguguggaagggccaucgaucaacggauaaaaguuac
cccggggauaacaggcugaucucccccgagcguccacagcggcggggagg
uuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguccc
aaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaa
cgucgugagacaguucggucucuauccgccacgggcgcaggaggcuugag
gggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuc
ccagcugucccuccaggggcauaagcuggguagccaugugcggaagggau
aaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuccc
acggcgucaagccgguaaggacccgggaagaccacccgguggaugggccg
gggguguaagcgccgcgaggcguugagccgaccggucccaaucguccgag
gucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wzd Structural insights into the translational infidelity mechanism.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): S14 E15 K16 K25 H31 T35 K36 T37 E38 K40 N41 E44 N55 T56 L57 H58 R60 K62 K63 K64 L66 Y69 L70 G71 K72 R73 P74 D75 K78 I80
• Binding residue (residue number reindexed from 1): S13 E14 K15 K24 H30 T34 K35 T36 E37 K39 N40 E43 N54 T55 L56 H57 R59 K61 K62 K63 L65 Y68 L69 G70 K71 R72 P73 D74 K77 I79

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4wzd, PDBe:4wzd, PDBj:4wzd
• PDBsum: 4wzd
• PubMed: 26037619
• UniProt: Q5SHP0|RL23_THET8 Large ribosomal subunit protein uL23 (Gene Name=rplW)