Structure of PDB 4v6g Chain DP Binding Site BS01

Receptor Information

>4v6g Chain DP (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Ligand information

>4v6g Chain DA (length=2886)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgcaaacgaaaaguccgcggccguggaccc
gaaaccgggcgagcuagcccuggccagggugaagcuggggugagacccag
uggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcu
aggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaug
acuuuagggucagccucaggcgcugacuggggccuguagagcacugauag
ggcuagggggcccaccagccuaccaaacccugucaaacuccgaagggucc
cagguggagccugggagugagggcgcgagcgauaacguccgcguccgagc
gcgggaacaaccgagaccgccagcuaaggcccccaagucugggcuaagug
guaaaggauguggcgccgcgaagacagccaggauguuggcuuagaagcag
ccaucauuuaaagagugcguaauagcucacuggucgaguggcgccgcgcc
gaaaaugaucggggcuuaagcccagcgccgaagcugcgggucugggggau
gaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccgc
gagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgaua
aagagggugagaaucccucucgccguaagcccaaggguuccuacgcaaug
gucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguag
ccgaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggg
ggacgcucuaggcuagggggaccggagccauggacgagcccggccagaag
cgcagggugggagguaggcaaauccgccucccaacaagcucugcguggug
gggaagcccguacgggugacaaccccccgaagccagggagccaagaaaag
ccucuaagcacaaccugcgggaacccguaccgcaaaccgacacagguggg
cgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucu
gcaaguuggccccguaacuucgggagaaggggugcucccuggggugauga
gccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaaca
cagcucucugcgaacucguaagaggagguauagggagcgacgcuugcccg
gugccggaaggucaaggggaggggugcaagccccgaaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucgg
cgagggacccggugaaauugaacuggccgugaagaugcggccuacccgug
gcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcucu
uggucgcgccugcguaggauaggugggagccugugaacccccgccuccgg
gugggggggaggcgccggugaaauaccacccuggcgcggcugggggccua
acccucggauggggggacagcgcuuggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgg
aaauccgccggagagcgcaaggguagaagggggccugacugcgaggccug
caagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugu
ggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcug
aucucccccgagcguccacagcggcggggagguuuggcaccucgaugucg
gcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgc
ccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgg
ucucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguac
gagaggaccggaagggacgcaccucugguuucccagcugucccuccaggg
gcauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucua
agcgggaagcccgccccaagaugaggccucccacggcgucaagccgguaa
ggacccgggaagaccacccgguggaugggccggggguguaagcgccgcga
ggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6g Structural aspects of messenger RNA reading frame maintenance by the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 L17 K18 K22 G23 Y26 Q46 A49 R56 K63 R67 F69 Y74 K76 K77 L79 E80 V81 R82 M83 G84 K85 G86 R101 H123 K124 P126 K128 Q141
• Binding residue (residue number reindexed from 1): R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 L17 K18 K22 G23 Y26 Q46 A49 R56 K63 R67 F69 Y74 K76 K77 L79 E80 V81 R82 M83 G84 K85 G86 R101 H123 K124 P126 K128 Q141

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:4v6g, PDBe:4v6g, PDBj:4v6g
• PDBsum: 4v6g
• PubMed: 20400952
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)