Structure of PDB 4v8d Chain DR Binding Site BS02

Receptor Information

>4v8d Chain DR (length=137) Species: 300852 (Thermus thermophilus HB8)

MNRGALIKLVESRYVRTDLPEFRPGDTVRVSYKVKEGNRTRIQDFEGIVI
RIRRNGFNTTFTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAKLY
FIRNLSDREIRRKLRADRKRIDQDRAAERAAKEEAQK

Ligand information

>4v8d Chain DA (length=2907)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcgcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccgaaaagu
ccgcggccguggacccgaaaccgggcgagcuagcccuggccagggugaag
cuggggugagacccaguggaggcccgaaccggugggggaugcaaaccccu
cggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcu
gguucuccccgaaaugacuuuagggucagccucaggcgcugacuggggcc
uguagagcacugauagggcuagggggcccaccagccuaccaaacccuguc
aaacuccgaagggucccagguggagccugggagugagggcgcgagcgaua
acguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccccc
aagucugggcuaagugguaaaggauguggcgccgcgaagacagccaggau
guuggcuuagaagcagccaucauuuaaagagugcguaauagcucacuggu
cgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagc
ugcgggucugggggaugaccccaggcgguaggggagcguucccgaugccg
augaaggccgacccgcgagggcggcuggagguaagggaagugcgaaugcc
ggcaugaguaacgauaaagagggugagaaucccucucgccguaagcccaa
ggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaaggug
aagccgaaaggcguagccgaagggcagccgguuaauauuccggcccuucc
cgcaggugcgauggggggacgcucuaggcuagggggaccggagccaugga
cgagcccggccagaagcgcagggugggagguaggcaaauccgccucccaa
caagcucugcgugguggggaagcccguacgggugacaaccccccgaagcc
agggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgca
aaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaacc
cucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggug
cucccuggggugaugagccccggggagccgcagugaacaggcucuggcga
cuguuuaccaaaaacacagcucucugcgaacucguaagaggagguauagg
gagcgacgcuugcccggugccggaaggucaaggggaggggugcaagcccc
gaaccgaagccccggugaacggcggccguaacuauaacgguccuaaggua
gcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgac
cggagcgcugucucggcgagggacccggugaaauugaacuggccgugaag
augcggccuacccguggcaggacgaaaagaccccguggagcuuuacugca
gccugguguuggcucuuggucgcgccugcguaggauaggugggagccugu
gaacccccgccuccgggugggggggaggcgccggugaaauaccacccugg
cgcggcugggggccuaacccucggauggggggacagcgcuuggcgggcag
uuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagguc
cccucaggcgggacggaaauccgccggagagcgcaaggguagaagggggc
cugacugcgaggccugcaagccgagcaggggcgaaagccgggccuaguga
accgguggucccguguggaagggccaucgaucaacggauaaaaguuaccc
cggggauaacaggcugaucucccccgagcguccacagcggcggggagguu
uggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaa
ggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacg
ucgugagacaguucggucucuauccgccacgggcgcaggaggcuugaggg
gggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuccc
agcugucccuccaggggcauaagcuggguagccaugugcggaagggauaa
ccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccac
ggcgucaagccgguaaggacccgggaagaccacccgguggaugggccggg
gguguaagcgccgcgaggcguugagccgaccggucccaaucguccgaggu
cuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8d A new understanding of the decoding principle on the ribosome.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): N2 R3 G4 A5 R23 R51 R53 R54 N55 N58 T60 I75 R95 R96 A97 K98 F101 K113 R115 K119
• Binding residue (residue number reindexed from 1): N2 R3 G4 A5 R23 R51 R53 R54 N55 N58 T60 I75 R95 R96 A97 K98 F101 K113 R115 K119

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

External links

• PDB: RCSB:4v8d, PDBe:4v8d, PDBj:4v8d
• PDBsum: 4v8d
• PubMed: 22437501
• UniProt: P60490|RL19_THET8 Large ribosomal subunit protein bL19 (Gene Name=rplS)