Structure of PDB 4v4p Chain AC Binding Site BS01

Receptor Information

>4v4p Chain AC (length=221) Species: 300852 (Thermus thermophilus HB8)

KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRS
DQNVRGTVSGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGW
MDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIK
AGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT
FLRSVYVTTTMGPSVRINPHS

Ligand information

>4v4p Chain AA (length=2872)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuugcgcggggggaaccuggggaacugaaacaucucaguaccca
gaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaagggg
accagccuaaaccguccggcuuguccgggcggggucguggggcccucgga
caccgaauccccagccuagccgaagcuguugggaagcagcgccagagagg
gugaaagccccguaggcgaaagguggggggauaggugaggguacccgagu
accccgugguucguggagccaugggggaaucugggcggaccaccgccuaa
ggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagg
ugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuu
acaagcagucacggccccgcaagggguuguggcgugccuauugaagcaug
agccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcg
uagggaaaccgaguccgaacagggcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcc
auccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaugcggggcuuaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
aggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
ggggggccacccuggcgcggcugggggccuaacccucggauggggggaca
gcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacgg
aggcgcccaaagguccccucaggcgggacggaaauccgccggagagcgca
aggguagaagggggccugacugcgaggccugcaagccgagcaggggcgaa
agccgggccuagugaaccgguggucccguguggaagggccaucgaucaac
ggauaaaaguuaccccggggauaacaggcugaucucccccgagcguccac
agcggcggggagguuuggcaccucgaugucggcucgucgcauccuggggc
ugaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcga
gcuggguucagaacgucgugagacaguucggucucuauccgccacgggcg
caggaggcuugaggggggcucuuccuaguacgagaggaccggaagggacg
caccucugguuucccagcugucccuccaggggcauaagcuggguagccau
gugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaa
gaugaggccucccacggcgucaagccgguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4p Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding.
• Resolution: 5.5 Å
• Binding residue (original residue number in PDB): K5 R6 Y7 K36 F37 K46 Q101 L104 M108 S125 K126 G128 R129 I130 L131 G132 P133 R134 D166 K167 T168 H172 K205 G206 S211 Y213 T217 M218 G219
• Binding residue (residue number reindexed from 1): K1 R2 Y3 K32 F33 K42 Q94 L97 M101 S118 K119 G121 R122 I123 L124 G125 P126 R127 D159 K160 T161 H165 K198 G199 S204 Y206 T210 M211 G212

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0006417 regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v4p, PDBe:4v4p, PDBj:4v4p
• PDBsum: 4v4p
• PubMed: 15802605
• UniProt: P27150|RL1_THETH Large ribosomal subunit protein uL1 (Gene Name=rplA)