Structure of PDB 8k2b Chain Lj Binding Site BS01

Receptor Information

>8k2b Chain Lj (length=38) Species: 9606 (Homo sapiens)

FKNKTVLKKRCKDCYLVKRRGRWYVYCKTHPRHKQRQM

Ligand information

>8k2b 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: 8k2b Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): F66 N68 K69 T70 L72 R75 K83 R84 R85 G86 W88 Y89 Y91 P96 R97 K99 R101 Q102 M103
• Binding residue (residue number reindexed from 1): F1 N3 K4 T5 L7 R10 K18 R19 R20 G21 W23 Y24 Y26 P31 R32 K34 R36 Q37 M38

Gene Ontology

Molecular Function

• GO:0005515 protein binding

Biological Process

• GO:0006412 translation
• GO:0032543 mitochondrial translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:0016604 nuclear body
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8k2b, PDBe:8k2b, PDBj:8k2b
• PDBsum: 8k2b
• PubMed: 38942792
• UniProt: Q9P0J6|RM36_HUMAN Large ribosomal subunit protein bL36m (Gene Name=MRPL36)