Structure of PDB 8xxm Chain SW Binding Site BS01

Receptor Information
>8xxm Chain SW (length=129) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFE
IIDDHRAGKIVVNLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSRQFGF
IVLTTSAGIMDHEEARRKHTGGKILGFFF
Ligand information
>8xxm Chain S2 (length=1723) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuuaacgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuuggcucucggccggggcccgaag
cguuuacuuugaaaaaauuagaguguucaaagcaggcccgagccgccugg
auaccgcagcuaggaauaauggaauaggaccgcgguucuauuuuguuggu
uuucggaacugaggccaugauuaagagggacggccgggggcauucguauu
gcgccgcuagaggugaaauucuuggaccggcgcaagacggaccagagcga
aagcauuugccaagaauguuuucauuaaucaagaacgaaagucggagguu
cgaagacgaucagauaccgucguaguuccgaccauaaacgaugccgaccg
gcgaugcggcggcguuauucccaugacccgccgggcagcuuccgggaaac
caaagucuuuggguuccggggggaguaugguugcaaagcugaaacuuaaa
ggaauugacggaagggcaccaccaggaguggagccugcggcuuaauuuga
cucaacacgggaaaccucacccggcccggacacggacaggauugacagau
ugauagcucuuucucgauuccgugggugguggugcauggccguucuuagu
ugguggagcgauuugucugguuaauuccgauaacgaacgagacucuggca
ugcuaacuaguuacgcgacccccgagcggucggcgucccccaacuucuua
gagggacaaguggcguucagccacccgagauugagcaauaacaggucugu
gaugcccuuagauguccggggcugcacgcgcgcuacacugacuggcucag
cgugugccuacccuacgccggcaggcgcggguaacccguugaaccccauu
cgugauggggaucggggauugcaauuauuccccaugaacgaggaauuccc
aguaagugcgggucauaagcuugcguugauuaagucccugcccuuuguac
acaccgcccgucgcuacuaccgauuggaugguuuagugaggcccucggau
cggccccgccggggucggcccacggcccuggcggagcgcugagaagacgg
ucgaacuugacuaucuagaggaaguaaaagucguaacaagguuuccguag
gugaaccugcggaaggaucauua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<..................<<.....
<<.<<<.....>>>.>>......>>.........<<<<...<<<<.....
...>>>>...>>>><<..<<<<<...<......>..>>>>>......>>.
..<<<<.<<<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<....>>.>...>>>>>>.........<<<....<<<<...>>>>..>>>
..>...>>.>.....<.<<<<<<<.<<<....>>>.>>.>>>>.>..>..
...<<..<...........>..>>.........<<<<<((....<.<<<<
.....<<..))>>.......>>>>>>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<.<<......<<.<.............>>>
...<<<<<<.<.......<<...<.......>.<<<<.......>>>>..
.>>......>.>>>..>>>........<.<<.<<<.<<<...........
....>>>.>>>.>>.>....>>....<<<<<<..<...<<<<..<<<.<<
<<<<<<...<<<......>>>......>>>>>>>>.>>>.......<<..
..>>...>>>>..>..>>>.>>>...>>>...>>.>....<<<<<<<...
<...<<<<.<.....>.>>>>...>>>>>>>>..........<<<.<<.<
<<..<.<<<<<<.<<<<......>>>>>>>>>>.>..>>>...<<..))>
>...>>.....>>>.>.>.<<<......<<<<....>>>>....>>>..)
))).]<<<<<.<<<<<<<..<<..<<<<<..<<<.<<<<<<......<<.
.......>>..........<<<<<.<....<<<<<<.......<<.<<<.
.......>>>.>>.....>>>>>>...<<.<<<..<<.<<<<<<....<<
<.<<<<<....>>>...<<<......>>>...>>.>>>....<<<...<.
..<<<<..<<<<<<<<<<<<.......>>>>.>>>>.....>>>>..>>>
>..>.....<<<<<.....>>>>>........>>>....>>>.>>>....
.>>>>>>>.....>.>>>>>...>>.>>>>.>>>.....<<.<<<.....
...<.......<<<.<<<<....>>>>.>>>....>.........>>>.>
>......<...<.<<<<<..........>>>>>>....>.....>>>>>.
....<<<<<<<<.......>>>>>>>>......>>...>>>>>>>>>>.>
>....<..<<.<..<<<<.<<.....<..<<<<.<<<..<<<<.<<...<
<<<<...<<.....................>>.....>>>>>...>>.>>
>>..>>>.>>>>.>.....>>.>>>>...>.>>...>.....<<<<<<<<
<....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8xxm Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		V2 R3 M4 V6 N16 K19 R20 R28 C30 S31 K32 H56 R57 K60 N70 K71 V74 I75 S76 R78 D80 Q82 L83 K88 W89 T105 T106 S107 H120 G122 K124 F130
Binding residue
(residue number reindexed from 1)		V1 R2 M3 V5 N15 K18 R19 R27 C29 S30 K31 H55 R56 K59 N69 K70 V73 I74 S75 R77 D79 Q81 L82 K87 W88 T104 T105 S106 H119 G121 K123 F129
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0008284 positive regulation of cell population proliferation
GO:0009615 response to virus
GO:0042274 ribosomal small subunit biogenesis
GO:0045787 positive regulation of cell cycle
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032040 small-subunit processome
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8xxm, PDBe:8xxm, PDBj:8xxm
PDBsum8xxm
PubMed38641729
UniProtP62244|RS15A_HUMAN Small ribosomal subunit protein uS8 (Gene Name=RPS15A)

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