Structure of PDB 5v8i Chain 2Q Binding Site BS01

Receptor Information

>5v8i Chain 2Q (length=141) Species: 262724 (Thermus thermophilus HB27)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDFGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

Ligand information

>5v8i Chain 2A (length=2858)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgucuaguccgcggccguggacccgaaaccgggcgag
cuagcccuggccagggugaagcuggggugagacccaguggaggcccgaac
cggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagc
uaaccgagcccggagauagcugguucuccccgaaaugacuuuagggucag
ccucaggcgcugacuggggccuguagagcacugauagggcuagggggccc
accagccuaccaaacccugucaaacuccgaagggucccagguggagccug
ggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccg
agaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugugg
cgccgcgaagacagccaggagguggcuuagaagcagccauccuuuaaaga
gugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaucgggg
cucaagcccagcgccgaagcugcgggucuggggccccaggcgguagggga
gcguucccgaugccgaugaaggccgacccgcgagggcggcuggagguaag
ggaagugcgaaugccggcaugaguaacgauaaagagggugagaaucccuc
ucgccguaagcccaaggguuccuacgcaauggucgucagcguaggguuag
gcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgguuaa
uauuccggcccuucccgcaggugcgauggggggacgcucuaggcuagggg
gaccggagccauggacgagcccggccagaagcgcagggugggagguaggc
aaauccgccucccaaaagcucugcgugguggggaagcccgcgggugacaa
ccccccgaagccagggagccaagaaaagccucuaagcacaaccugcggga
acccguaccgcaaaccgacacaggugggcgggugcaagagcacucaggcg
cgcgggagaacccucgccaaggaacucugcaaguuggccccguaacuucg
ggagaaggggugcucccuggggugaugagcuccggggagccgcagugaac
aggcucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaag
aggagguauagggagcgacgcuugcccggugccggaaggucaaggggagg
ggugcaagccccgaaccgaagccccggugaacggcggccguaacuauaac
gguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaa
aagcguaacgaccggagcgcugucucggcgagggacccggugaaauugaa
cuggccgugaagaugcggccuacccguggcaggacgaaaagaccccgugg
agcuuuacugcagccugguguuggcucuuggucgcgccugcguaggauag
gugggagccugugaacccccgccuccgggugggggggaggcgccggugaa
auaccacccuggcgcggcugggggccuaacccucggauggggggacagcg
cuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacggagg
cgcccaaagguccccucaggcgggacggaaauccgccggagagcgcaagg
guagaagggggccugacugcgaggccugcaagccgagcaggggcgaaagc
cgggccuagugaaccgguggucccguguggaagggccaucgaucaacgga
uaaaaguuaccccggggauaacaggcugaucucccccgagcguccacagc
ggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcuga
agaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcu
ggguucagaacgucgugagacaguucggucucuauccgccacgggcgcag
gaggcuugaggggggcucuuccuaguacgagaggaccggaagggacgcac
cucugguuucccagcugucccuccaggggcauaagcuggguagccaugug
cggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaagau
gaggccucccggcagccgguaaggacccgggaagacgacccgguggaugg
gccggggguguaagcgccgcgaggcguugagccgaccggucccaaucguc
cgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v8i Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K18 K22 G23 G24 Y26 W41 Q46 A49 R56 R59 R60 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 G86 K87 R101 H123 K124 P126 K128
• Binding residue (residue number reindexed from 1): R5 R6 K8 Y9 K11 Q12 Q13 R14 G15 R16 K18 K22 G23 G24 Y26 W41 Q46 A49 R56 R59 R60 R67 F69 D71 Y74 K76 K77 E80 R82 M83 G84 G86 K87 R101 H123 K124 P126 K128

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:5v8i, PDBe:5v8i, PDBj:5v8i
• PDBsum: 5v8i
• UniProt: Q72I11|RL16_THET2 Large ribosomal subunit protein uL16 (Gene Name=rplP)