Structure of PDB 8fkv Chain LT Binding Site BS01

Receptor Information

>8fkv Chain LT (length=109) Species: 9606 (Homo sapiens)

SGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVY
KAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRI
RVMLYPSRI

Ligand information

>8fkv Chain L3 (length=2213)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggaacgggugggguccgcgcaguccgcccggagga
uucaacccggcggcgccgggcgcauuuccaccgcggcggugcgccgcgac
cggcuccgggacggcugggaaggcccggcggggaagguggcucgggcccg
aguguuacagcccccccggcagcagcacucgccgaaucccggggccgguc
ggcggcgacgucggcuacccacccgacccgucuugaaacacggaccaagg
agucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgc
aaggugggaucccgaggcccaguccgccgagggcgcaccaccggccgcac
gagcgcacguguuaggacccgaaagauggugaaaccaucuaguagcuggu
ucccuccgaaguuucccggauagcuggcgcucuccgcaguuuuauccggu
ggguaagaagccggcguggaaugcgagugccuagugggccacuuuuggua
agcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccga
ugccgacgcucaucagaccccagaaaagguguugguugauauagacagca
ggacgguggccauggaagucggaauccgcuaaggaguguguaacaacuca
ccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcc
cauacccggccgucgccggcagucgagaguggacggccgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcauuca
aacgagaacuuugaaggccgaaguggagaaggggcgauggccuccggccc
ucgcggagaugggcgccgcgaggcguccagugaaucucgcccgcagcagg
ucuccggugaacagccucuggcaauguagguaagggaagucgggaauccg
auucccacugucccuaccuacuauccagcgaaaccacagccaagggaacg
ggcuuggcggaaucagcggggagaagacccuguugagcuugacucuaguc
uggcacggugaagagacaugagagguguagaauaagugggaggcggccgc
cggugaaauaccacuacucugaucguuuuuuccagugccagguggggagu
uauccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuacc
acagggauaacuggcuuguggcggccaagcgcgacgucgcuuuuugauga
ugucggcucuuccuaucauugugaagcagaauucaccaagcguuggauug
uucacccacuaauagggaacgugagcuggggaccgucgugagacagguuc
ccuacugaugguuguugccaugguaauccugcucaguacgagaggaaccg
cagguucagacauuugguggugcuuggcugaggagccaauggggcgaagc
uaccaucugugggauuaugacugaacgccucuaagucagaaucccgccca
ggcggaacgauaagcgccgcggagccucgguuggccucggauagccgguc
cccgggguccggugcggagugcccuucguccugggaaacggggcgcggcc
ggagaggcggccgcccccucgcccgucacgcaccgcacguucguggggaa
ccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgu
acguagcagagcagcucccucgcugcgaucuauugaaagucagcccucga
cacaaggguuugu

........................<<<<<<...............>>>>>
.>.........<<....>>..<<<<<<.....<<.....>>....>>>>>
>..<<<..<<<<<...<<<<<<<<<<.>>>>>>.>>>>.....>>>>>..
<<<<<<<<<<...<<<<<<<<.<<.....<<<<<<<<....<<<<.....
.>>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>
>>>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....
<<<<<<.>>>>>>..>>>................................
..<<....>>...............<<<<....>>>>.............
...................<<<<<<<<..<<<......<<<<<<<<.<<<
.....<<<<<<<.>>>>>>>......>>>.>>>.>>>>>..<<<<<<<<<
<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<......<<<<<<..>>>
>>>.......>>>>>>.>>>........>>>>>>..>>>>>>>>>>>>>>
.>>>>>>....>>>...>>>>>>>>..<<<<.<....>.>>>><<<<<<.
...<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>>>..
..<<<<<...<<<..<<.........>>..>>>....>>>>>.<<.>>..
..>>>>>>>>>>>>>..<<.<...<<<<<<...>>>>>>......>.>>.
.<<<<<<......<<<.>>>..<<.<<<<<<<...<<<.<<<<<<<<...
>>>>>>...<<..>>....>>>>>>>>>>>>..>>..<<<<.<<<<<...
..>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((...
....<<<<<.....<<..........<<<.<<<<<<<<<<.....<.<<<
<<.<<....<<.........>>....>>.........<<......>>...
>>>>>.>.>>>>>>>>>>>>>..........))).>>...>>>>>..>>>
...>>>>>>><<<<<<.<<<.............<<..>>..........>
>>>>>>>>....>>>>>>...<<<<<<<<.<<......<<<<.<<<<...
.>>>>>>>>...>>>>>>>>>>........>>>>>><<.....<<.<<<<
<<.......>>>>>>.<<<<....<<<<...<<<<...........>>>>
..<<<<<...<<<<<<<....>>>>>>>......>>.>>><<......>>
.>>>><<<.....>>>..>>>>...<<<<<<.<<<<<<<<..<<<<<<.>
>>>>>.>>>.>>>>>>>>>>>......>>....>>...<<<<<<......
..>>>>>>....<<<<.<<<<......<<<<<<.<<<<<<.<<<<<.<<<
<<<<<<...<<<<<<<<<<.<<<<..........<<<<<..<<<.>>>..
..........>>>>>.>>>>.>>.>>>>>>>>..>>>>>>>>>..>>>>>
...<<<<<<<..<<<.........>>>>>>>>>>........>>>>>.>.
>>>>>>.............<<<<<<...<..>...>>>>>>.......((
...<<<<<<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<....
.))..>>>.....>>>>>....>>>>>>..<<<<<<<....>>>.>>>>>
>>>.>>>>..<<<<<<.<..<<<..<.<<<<<.................>
>>>>.><<<<....<<<<.<<.<<<<<<<....>>>>>..>>.>>...>>
>>...>>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>
...>.>>>>>>.<<<<<<<.<<..<<<<....<<<........<<<<<.<
<<<>>>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<<<<
<......>>>>>>>>>>>...>>>>..>>>..............>>>>..
>>>>>>>>><<<<<.<.............>....<<.<<<<<<<.<<...
..<<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>
>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkv Principles of human pre-60 S biogenesis.
• Resolution: 2.47 Å
• Binding residue (original residue number in PDB): S2 G3 R4 W6 K8 K15 R16 L18 R19 N20 Q21 R22 E23 H24 Y34 R36 G44 Y51 K52 K54 N55 V58 P60 P64 T67 R68 V69 W71 K73 R76 H78 G79 N80 S81 R85 K87 R89 S90 N91 P93 A94 R100 R102 R109
• Binding residue (residue number reindexed from 1): S1 G2 R3 W5 K7 K14 R15 L17 R18 N19 Q20 R21 E22 H23 Y33 R35 G43 Y50 K51 K53 N54 V57 P59 P63 T66 R67 V68 W70 K72 R75 H77 G78 N79 S80 R84 K86 R88 S89 N90 P92 A93 R99 R101 R108

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8fkv, PDBe:8fkv, PDBj:8fkv
• PDBsum: 8fkv
• PubMed: 37410842
• UniProt: P18077|RL35A_HUMAN Large ribosomal subunit protein eL33 (Gene Name=RPL35A)