Structure of PDB 4v4p Chain AD Binding Site BS01

Receptor Information

>4v4p Chain AD (length=173) Species: 300852 (Thermus thermophilus HB8)

QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNL
KVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGT
SAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEVGNGGRTDKPFVKAGN
KHHKMKAPNVRGVAMNAVDHPFG

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): Q60 I63 F66 D69 Y82 D83 P84 R86 A96 D97 G98 K146 P147 G148 R149 G151 Q152 L153 V154 R155 A157 G158 L175 S177 L184 N196 G198 T200 F204 K206 A207 K210 H211 H212 V224 R225 G226 V227 M229 N230 V232 D233 H234 P235
• Binding residue (residue number reindexed from 1): Q1 I4 F7 D10 Y23 D24 P25 R27 A37 D38 G39 K87 P88 G89 R90 G92 Q93 L94 V95 R96 A98 G99 L116 S118 L125 N137 G139 T141 F145 K147 A148 K151 H152 H153 V160 R161 G162 V163 M165 N166 V168 D169 H170 P171

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit

External links

• PDB: RCSB:4v4p, PDBe:4v4p, PDBj:4v4p
• PDBsum: 4v4p
• PubMed: 15802605
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)