Structure of PDB 8xt1 Chain Sf Binding Site BS01

Receptor Information

>8xt1 Chain Sf (length=370) Species: 9606 (Homo sapiens)

VARYPPIVASMTADSKAARLRRIERWQATVHAAESVDEKLRILTKMQFMK
YMVYPQTFALNADRWYQYFTKTVFLSGLPAALRAVACDCLLQEHFYLRRR
RRVHRYEESEVISLPFLDQLVSTLVGLLSPHNPALAAAALDYRCPVHFYW
VRGEEIIPRGHRRGRIDDLRYQIDDKPNNQIRISKQLAEFVPLDYSVPIE
IPTIKCKPDKLPLFKRQYENHIFVGSKTADPCCYGHTQFHLLPDKLRRER
LLRQNCADQIEVVFRANAIASLFAWTGAQAMYQGFWSEADVTRPFVSQAV
ITDGKYFSFFCYQLNTLALTTQADQNNPRKNICWGTQSKPLYETIEDNDV
KGFNDDVLLQIVHFLLNRPK

Ligand information

>8xt1 Chain L1 (length=1500)

gcuaaaccuagccccaaacccacuccaccuuacuaccagacaaccuuagc
caaaccauuuacccaaauaaaguauaggcgauagaaauugacuggcgcaa
uagauauaguaccgcaagggaaagaugaaaaauuauaaccaagcauaaua
uagcaaggacuaaccccuauaccuucugcauaaugaauuaacuagaaaua
acuuugcaaggagagccaaagcuaagacccccgaaaccagacgagcuacc
uaagaacagcuaaaagagcacacccgucuauguagcaaaauagugggaag
auuuauagguagaggcgacaaaccuaccgagccuggugauagcugguugu
ccaagauagaaucuuaguucaacuuuaaauuugcccacagaaccaaaucc
ccuuguaaauuuaacuguuaguccaaagaggaacagcucuuuggacacua
ggaaaaaaccuuguagagagaguaaaaaauuuaacacccauaguaggccu
aaaagcagccaccaauuaagaaagcguucaagcucaacacccacuaccua
aaaaaucccaaacauauaacugaacuccucacacccaauuggaccaaucu
aucacccuauagaagaacuaauguuaguauaaguaacaugaaaacauucu
ccuccgcauaagccugcgucagaucacacugacaauuaacagcccaauau
cuacaaucaaccaacaagucauuauuacccucacugucaacccaacacag
gcaugcucauaaggaaagguuaaaaaaaguaaaaggaacucggcaaaucu
uaccccgccuguuuaccaaaaacaucaccucuagcaucaccaguauuaga
ggcaccgccugcccagugacacauguuuaacggccgcgguacccuaaccg
ugcaaagguagcauaaucacuuguuccuuaaauagggaccuguaugaaug
gcuccacgaggguucagcugucucuuacuuuuaaccagugaaauugaccu
gcccgugaagaggcgggcauaacacagcaagacgagaagacccuauggag
cuuuaauuuauuaaugcaaacaguaaccugcauuaaaaauuucgguuggg
gcgaccucggagcagaacccaaccuccgagcaguacaugcuaagacuuca
ccagucaaagcgaaccucaauugauccaauaacuugaccaacggaacaag
uuacccuagggauaacagcgcaauccuauucuagaguccauaucaacaau
aggguuuacgaccucgauguuggaucaggacaucccgauggugcagccgc
uauuaaagguucguuuguucaacgauuaaaguccuacgugaucugaguuc
agaccggaguaauccaggucgguuucuaucuacuuuaaauuccucccugu
acgaaaggacaagagaaauaaggccuacuucacaaagcgccuucccccgu
aaaugauaucaucucaacuuagauacccacacccacccaagaacaggguu

<<<.......<<<<....................................
.<......>.........<.....<<.....>>....>.....>>.>>..
...........<<....>>......................>>>......
.....<<<.......>>>...<.<........>.>.<<<<<<........
.<<<.<<..<<....>>...>>.>>>...<<.<...<<<<.<.....<<<
<<.<<<..<<<.....>>>...<<<..<<<<........>>>>.>>>...
.>>>.>>>>>...<<.......>>......>.>>>>......>.>>..<<
<<<<....<<<<....>>>><<<.<<<<<<<<<<.....<<......>>.
....>>>>>>>>>>..>>>.<<<<<<<<<<......>>>>>>>>>>...<
<<......>>>....<<<.<<<...<..............<....<<<..
.......>>>....>.......<<<......>>>................
....................>...>>>>>>........>>>>>>...<<<
<<......>>>>>.........>>>>>><......<<..<<<....>>><
<<<..<<<<........<<<<<......>>>>>......<<<...<<<<.
......................>>>>.......>>>.....<<......>
>.>>>>.....>>>>..<<<<...<<<<<<<<.<<.........<.....
.<<<<<<..<<<.........>>>...<<<<<<.............>>>>
>>....<<<.<<<..<<<<<....>>>..>>>>><<<<<<......>>>>
>>........<...........<<<<<<.....>>>>>>.....>....>
>>....>>.>>>>.....>..>>.>>>>>>>>>>>>.>>.....>.....
<<<<<........>>>>>.......<<..<<<.<<......<<<<.<<<<
<<..<<<<<.<<<<<<<<..........>>>>>>>>>>>>>..<<<<...
..>>>><<<<<<...........>>>>>>..<<.....<<<..<<<<...
..>>>>..>>>....>>.........<<<....>>>............>>
>>..>>>>>>.......<<<..<.<<<<<<...<<.......>>...>>>
>>>...>.>>.>.......<<<<<.<<<<<<..<<.<<<<<<......>>
>>>>...>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>...
.<<<<<<<....>>>.>>>>....>>..>>>.>>....<<<.<<<.....
............>>>.>>><<<<<...<<<....>>>.>>>>>......<
<<................>>>.............<<<<.......>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8xt1 Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): A49 S50 T52 A53 D54 S55 K56 A57 R59 R62 I63 W66 R81 K85 M86 Q87 M92 Y94 T97 F98 R162 H164 R165 Y166 R219 G220 H221 R222 R223 R225 K270 P272 F274 Q277 R310 R313
• Binding residue (residue number reindexed from 1): A9 S10 T12 A13 D14 S15 K16 A17 R19 R22 I23 W26 R41 K45 M46 Q47 M52 Y54 T57 F58 R102 H104 R105 Y106 R159 G160 H161 R162 R163 R165 K210 P212 F214 Q217 R250 R253

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0006915 apoptotic process
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xt1, PDBe:8xt1, PDBj:8xt1
• PDBsum: 8xt1
• PubMed: 38942792
• UniProt: Q9NP92|RT30_HUMAN Large ribosomal subunit protein mL65 (Gene Name=MRPS30)