Structure of PDB 4v8p Chain DL Binding Site BS01

Receptor Information

>4v8p Chain DL (length=108) Species: 5911 (Tetrahymena thermophila)

AQRITYRRRCSYNTRSNKVRKVKTPGGRLVAQYVKKVVNYTKCSEAGCNV
ALNGIAQVRPAEYATIARSAKTVSRVYGGELCHTCVRSRIIRAFLTEEVK
IVKRKMIS

Ligand information

>4v8p Chain D1 (length=3119)

cuacaccugaaacaagcaagauuacccgcugaacuuaagcauaucaguaa
gcggaggaaaagaaacuaacuaggauagccccaguaauggcgaaugaaca
ggcuaaagcucaaagugaaaaucugaaguggucaacacaacagaauugua
aucuaaagggucaaccugaaacuaagcuccucucauaaguuccuuggaac
aggacgucaaagagggugacaaccccguagucggagaggaaggcuggugu
aagggagauuucaaagagucggguuguuugggauugcagcccuaaguggg
agauaaacuucuucuaaagcuaaauauacacgggagaccgauagcgaaca
aguacugcgaaggaaagaugaaaagaacuuugaaaagagggcuaaaagac
uugaaaccguugagaaggaagcuguagaagagcaauaaacuggacggcgc
auaagggggaaguacuaaucacugcagagucgauacguaaaaggucgaug
aguaaggaaaugguacagaacuugcuacgccggucagaagacaaaauggg
uucagauugaaggagucaccugagaucgggcagcaaugcagaucaaaagg
aaaacuucaaacuggacugaggggccuaagggcgauuuugucaaaauggc
uucuacugacccgucuugaaacacggaccaaggagucuaucaauuaagcg
agugauaggguggaaaaacccguccgcgaaacgaaagugaguacaaggug
ccaagccgcaagguagcagcaucacccgaccuugagucuccgacgaaggg
uucgaggaagagcuuaauuguuaggacccgaaagauggugaacuacgcuu
gaauagggugaagccaggggaaacucugguggaagcucguagcgauacug
acgugcaaaucguucgucaaauuugaguguaggggcgaaagacuaaucga
accaucuaguagcugguucccuccgaaguuucucucaggauagcaagagc
aaguacgcaguuuuauuagguaaagcgaaugauuagaggacucgggguuc
caagaaucucgaccuauucucaaacuuuaaauugguaagagccgcggagu
uuacuuaaaugaacucucgggaagaaugcagugcucuuagugggccauuu
uugguaagcagaacuggcgaugagggaugaaccuaacguugagauaaggc
gcccaaaugcacgcucaucagauaccacaaaagguguugguucauacgga
cagcaggccugccgaaugaacuagcccugaaaauggauggcgcugaagcg
uguugccgauacucaaccaucagagcaaaugcgaggcuuugaugaguagg
agggcgugaucguugccuagaaguauugggcgugagccuauauggagcag
cgauuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagaccgaaguggagaaggguuccaugagaacagcaauuguucaugggu
uacucgauccuaagacauagguuaacuccuugcaauacaagaagacauuc
guuuucguugucaaaagggaaugagguuaauauuccucaagcuggacgug
guauagagcgguaacgcaaagaaacccggagacgucagcaggugucacug
gaagaguuaucuuuucuuuuuaacauacuauggccaugaaauuggauuau
ccagagauaucggcuguauguauggcagagcagcucagagcugucaguug
cgcaccugaugacccuugaaaaucugggggagacauaauuucacgccagu
ucguacccauaaccgcaucaggucuccaagguuagcagccucugguccau
agaacaauguagauaagggaagucggcaaauuggauccguaacuucggga
uaaggauuggcucugaggaucucagaacugaagcggacaaagguaauccg
acuguuuaauaaaaacaaagcauugugacggccucaacaggugaugacac
aaugugauuucugcccagugcucugaaugucaaagugacgcaauucaacc
aagcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaa
ugccucgucaucuaauuagugacgcgcaugaauggauuaaugagauuacc
acugucccuaucuacuaucuagcgaacccacagcuaagggaacgggcuua
gaauaaucagcggggaaagaagacccuguugagcuugacucuagucuaac
uuugugaaauggcagucauuuugcuuauuucgugaagaaaagacuggugc
aaaccaguucuaaaguuaaggucauuuauugacugauuuuugcgaaagac
augguuagggggggaguuugucuggggcggaaugccuguuaaaccauaac
gcaggcguccuaaguguagcucagugagaacggaaaucucacguagaaca
aaaggguaaaagcuacauugauuuugauuuucaguaggaauacaaaccgc
gaaagcguggccuaucgauccuuuaacuuuacaaguuuuaagcuagaggu
gucagaaaaguuaccacagggauaacuggcuuguggcagccaagaguuca
uaucgacguugcuuuuugauccuucgaugucggcucuuccuaucauugug
aagcagaauucacaacgugucggauuguucacccgcuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaa
acgauguugcgacaguaauuuaaguuaguacgagaggaacacuuaaauca
gauaauugguaaauacgguugucugaaaagacaaugccgugaagcuacca
ucuguuggauuaugacugaaggccucuaagucagaauccaugcuggaaag
caaugucuaagugugaugauaaacgaaaaaaaauaaaaauuaaguucgaa
agguagagcggggaagagcgaaaaagcuugaccuuaacugcuaaucguaa
uuccaaauuaucaucuacguaaaucuuuuguagacgacuuaacauggaac
ggguauuguaagcaugagaguagaauuuccuacgaucugcugagauucag
cccgucuccuuagauuuau

........................<<<<<<.....<......>......>
>>>>.>...{.....<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[...........<<<<..<<<.....>>>..>>>>......
.......<<<<<..<<<...<<<.<<<<<<<<<<......<<<<......
>>>>.((......<<<.....))>>>.......>>>>>>>..>>>>>>..
.>>>..>>>>.>........<<<<<<<........>>>>>>>.....(((
((..<<<<<<)))))..]]]....}.........................
....<<....>>...............<<<<....>>>>...........
.....................<.<<<<<<<....<<...<<<<.<<<<<.
....<<<....<<<<<.<<..<<<<...<<<<<<.<......>>>>>>>.
.>>.>>...>>>>>>>....>>>....>>>>>.>>>>..<<<<<<<<.<<
<<<<<.<<<<<<......<<<..<<<<..<<<....>>>.>>>>...>>>
....>>>>>>.>>>>>>>.....<<<....>>>.>>>>>>>>...>>..>
>>>>>>.>..<<<<........>>>><<<<<<...<<<<.<<<<<<<<<.
.<<<...<<<<......>>>>...>>>...<<....>>........<<<<
<...<<<....>>>....>>>>>.<<<<<<<....<<<...>>>....>>
.>>>.>>....>>>>>>>>>.>>>>.<<.<...<<<<<<.....<<<<<<
<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<<.<<.<
<........>>>>>>>>....>>>>>>>>>...<<.......>>......
>>>>>>......>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<
<.....<<<.<<<<<<<<<...<<<....<<<....<<<..<<<<<<<<<
...>>>>>>>>>>>>....>>>..>.>>...>>>>>>>...<<<.<<<<<
<..........>>>>>>>>>....>>>>>..>>>>>>>.>>..<<<<.<<
<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<....<<<
(((.....<<<<<<......<..........<<<.<<<<<<<<<......
..<<<<..>>>>....>>>>>>>>>>>>..........))).>....>>>
>>>.>>>....>>>>>><<<<<<<<<.........>>>>>>>>>....>>
>>>><.<<<<<<<<<<......<<<<.<<<<....>>>>>>>>...>>>>
>>>>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>
>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<<..<<<......>>>..........<<<<<<....
>>>>>>...>>>....>>>..<<<<<........>>>>>))<<<<.<<<<
..<<...<<<....>>>.......<<<<<<...<<<<.<<<<<<<<<<<<
<<<<<<.......>>>>>><...<<<<<...<<<<<<<....<<<<...>
>>>....>>>.>>>>....>>>>>....><<<<<<<.>>>>>>>>>>>.>
.>>>>>>>.>>>>.........>>>>>>.........>>..>>>>>>>>.
>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<
<<<.....<<<<<<<.<<...............<<<<<............
...>>>>><<.<<<<<<...>>>>>>.>>............<<<<<<<<<
..<<<.........>>>..<<<<<<<....<<<<....>>>>......>>
>>>>>...<<..<<<..<<<<<<....<<<.....<<<......>>>...
..>>>.>>>>..>>>>><<<<<<.......>>>>>>........<.....
......<<<<<.......>>>>>.....>.....>>....>>.>>>>>>>
.....>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>
>....(((((..{{{.{{......[[[[.{{[[[[..<<<<<..<<<<<<
<..<<<<<<<<<<.>>>>>>>>>>...<<<<<.....<<<<..<<<<<..
..>>>>>............<<<<<.....>>>>>..>>>>..>>>>>...
..>>>>>>>...>>>>>...<<<.....>>>..<<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
..(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<
....>>>.>>))).......(((((.[.(((.>>>>>>)))].)))))..
........]]]]..}}]]]].......<<.<...<<<<<<...<<.....
..>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<<<<<<<
<<......>>>>>>>..>>.<<<.........>>>.....>>>>>..>..
.>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.)))))...
..<<<<<<<<..<<<<.<<<<<<<<...............>>>>>>>><<
<<<...<<<<....<<<<<<<<<<....>>>>>..>>>>>...>>>>..>
>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>
>>>>>>>.....<<<<<<<<......<<................>>....
..<<<<...<<<...<<<<......>>>>..>>>...>>>>.........
......>>>>>>>>....<<<<<<<<...................<<<<<
<<<.<<<....<<<.<<..<<<<......>>>>..>>>>>...>>>....
>>>>>.>>>..>>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8p Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6.
• Resolution: 3.52 Å
• Binding residue (original residue number in PDB): A2 R4 I5 T6 Y7 R8 R9 R10 C11 S12 Y13 N14 T15 R16 S17 K19 R21 K22 V23 K24 T25 P26 G27 R29 L30 Q33 V35 K36 K37 V38 V39 N40 S45 A47 G48 N54 G55 I56 Q58 P61 A62 Y64 A65 T66 R69 K72 S75 R76 V77 Y78 E81 H84 R90 R93
• Binding residue (residue number reindexed from 1): A1 R3 I4 T5 Y6 R7 R8 R9 C10 S11 Y12 N13 T14 R15 S16 K18 R20 K21 V22 K23 T24 P25 G26 R28 L29 Q32 V34 K35 K36 V37 V38 N39 S44 A46 G47 N53 G54 I55 Q57 P60 A61 Y63 A64 T65 R68 K71 S74 R75 V76 Y77 E80 H83 R89 R92

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8p, PDBe:4v8p, PDBj:4v8p
• PDBsum: 4v8p
• PubMed: 22052974
• UniProt: P0DJ23|RL34_TETTS Large ribosomal subunit protein eL34 (Gene Name=RPL34)