Structure of PDB 4v6u Chain Bb Binding Site BS01

Receptor Information

>4v6u Chain Bb (length=127) Species: 186497 (Pyrococcus furiosus DSM 3638)

EKEFKRLLRVRARLKRKKPRFLRQEWWRYPKFKNDPKWRRPKGIDSKMRL
KLKGKPRSPSIGWSSPKLVRGLHPSGYEEVLVHNVKELEALDPKRQAARI
AHTVGKKKRIEIIKRAEELGIKVLNPR

Ligand information

>4v6u Chain B1 (length=3049)

gggcuaggacgcuaagccgcccgguggauggcucggcucggggcgccgac
gaagggcguggcaagcugcgauaagccccggcgaggcgcaggcagccguc
gaaccggggauucccgaaugggaccucccgcggcuuaugccgcacuccgg
gguuuauccccggagggggaacgcggggaauugaaacaucuuaguacccg
caggaaaagaaagcaaaagcgaugccgugaguaggggcgaccgaaaacgg
cagagggcaaacugaaccccgggccgacgagguucgggggaugugggguu
guagggcccccguaugagacccucgcgggugaagccgaaguccgcuggaa
cgcggcgccggagagggugauagccccguaggcguaagcccgcagggucu
cgggggacccugaguaccgucgguuggauauccggcgggaagcugggagg
caucggcucccaacccuaaauacgucccgagaccgauagcgaacuaguac
cgugagggaaagcugaaaagcaccccgggaggggggugaaaagagccuga
aaccgggcggcgauaggagggugcggcccgaaaggaaugagccuccccga
aggaaaccgcggcgacgcgggaguacgaggggaggggaccgggguugcac
cguccgucuugaaacacggggcagggaguucgcggccguggcgagguuaa
ggggguuaagccccguagccgcagggaaaccgacaugcccgcagccgggc
uuaugcccggugaggggcggggugcgaaagcgcccggagucacggccgcg
agacccgaaaccggucgaucuagcccggggcagggugaagucccucaacc
gagggauggaggcccgcuaggggugcugaugugcaguucgcucccgugac
cccgggcuaggggugaaaggccaaucgaggccggagauagcugguucccg
ccgaaucaucccgcaggauggccuccccggagguaggcggugggguagag
cacugauuggaggugcagggggcgaaagcccccggccuccugucaaacuc
cgaacccaccgccgccguagauggggggaguaggguggcgguguaagccg
uccaccgagaggggaacaacccagaccgggguuaaggccccaaagugccg
gcuaaguguuacuccaaagggugucccgggccuuagacagcggggaggua
ggcuuagaagcagccauccuuuaaagagugcguaacagcucacccgucga
gguccggggccccgaaaauggacggggcucaagccggccgccgagacccc
ggcgcacggaccgauugguccgugaucggguaggcgggcgugccgguggc
guagaagccgggccguaagguccgguggagccgccgguaucgcggauccu
gccgggaguagcagcguagucgggugagaaucccgaccgccggaggggcc
aggguuccacggcaauggucgucagccguggguuagucgguccuaacccc
gcccguaacucggcgcgggggaaagggaaacggguuuauauucccguacc
gcggggguaggugcggcaacgcaagcccggagggugacgccucgggguag
gcggaccggccgaugaggccggcuaagcguauaagcccggggagugccgu
aauggcgagaaccgggugaaagcgcgaauggcccccccguuagggggguu
ccgccgaucccuggggcccgugaaaagcccuccgggaauuccgauccccc
gcgaccguaccgagaaccgacacaggugccccugggugagaagccuaagg
cgugucgggggaaacccggccgagggaacucggcaaacuggccccguaac
uucgggagaaggggugccugcgggugcguaacccgcaggucgcagugacu
aggggggcccgacuguuuaauaaaaacacaggucccagcuagcccgaaag
gguuuguacuggggccgacgccugcccagugccgguaugugaagcccggg
uacaaccgggugaagcaccgguaaacggcggggguaacuauaacccucuu
aagguagcgaaauuccuugucgguuaaaugccgaccugcaugaauggcgu
aacgagguccccgcuguccccggccggggcccggcgaaaccucugccugg
cgcgcaugccagggacccccggugggaagcgaagaccccauggagcuuua
cugcagccugccguugccacacggcggggggugcgcagcguaggcgggag
gcgucgaagcccggccuccgggucggguggagccguccaugagacaccgc
ccacuccccgcuguguggcuaacccccgaaaggggggacagcgguaggug
ggcaguuuggcuggggcggcacgccuccgaaaagguaucggaggcgcccu
aaggucggcucaggcgggucaggaauccgccguagagugcaagggcaaaa
gccggccugacuggacccguaacagaggcggguccagccccgaaagggug
gccuagcgaaccccugugccuccccggugggggccagggaugacagaaaa
gcuacccuggggauaacagagucgucucgggcgagagcccauaucgaccc
cgaggcuugcuaccucgcugucggcucuucccauccuggcccugcagcag
gggccaaggguggggguguucacccauuaaaggggaacgugagcuggguu
uagaccgucgugagacaggucggaugcuaucuaccggggguguuggccgc
cugaggggaaggugccccuaguacgagaggaacagggugccgcggccucu
ggucuaccgguuguccucccgggcaucgccgggcagcuacgccgcagccg
auaaggccugaaagcaucuaaggccgaagcggcccccgaaaauaggcggc
cguucccuggcgcuugggccugggcgaccggcccauugccagggacgagg
gcucggguagaagacccgguugauagggcggggauguaagcgggaagggu
caaccgacccgcuuaguccgccgccccuaaucgcccgagguccugcccc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6u Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution.
• Resolution: 6.6 Å
• Binding residue (original residue number in PDB): R11 R13 R18 P21 R22 R25 Q26 E27 W29 R30 P32 K33 F34 W40 G45 I46 D47 S48 K49 R51 K55 G56 K57 P58 I63 G64 W65 S66 S67 P68 K69 R72 G73 L74 H75 P76 S77 L83 R101 I102 A103 H104 T105 G107 K108 K109 K110 K124 L126
• Binding residue (residue number reindexed from 1): R9 R11 R16 P19 R20 R23 Q24 E25 W27 R28 P30 K31 F32 W38 G43 I44 D45 S46 K47 R49 K53 G54 K55 P56 I61 G62 W63 S64 S65 P66 K67 R70 G71 L72 H73 P74 S75 L81 R99 I100 A101 H102 T103 G105 K106 K107 K108 K122 L124

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6u, PDBe:4v6u, PDBj:4v6u
• PDBsum: 4v6u
• PubMed: 23222135
• UniProt: Q9HH82|RL32_PYRFU Large ribosomal subunit protein eL32 (Gene Name=rpl32e)