Structure of PDB 9bkd Chain Z Binding Site BS01

Receptor Information
>9bkd Chain Z (length=227) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIII
LATRTQNVLGEKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIA
QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSM
KFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPTGKIGP
KKPLPDHVSIVEPKDEILPTTPISEQK
Ligand information
>9bkd Chain A (length=1672) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucugaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucguacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccccuucgcggggggga
ugcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacg
ccccccguggcggcgacgacccauucgaacgucugcccuaucaacuuucg
augguagucgccgugccuaccauggugaccacgggugacggggaaucagg
guucgauuccggagagggagccugagaaacggcuaccacauccaaggaag
gcagcaggcgcgcaaauuacccacucccgacccggggagguagugacgaa
aaauaacaauacaggacucuuucgaggcccuguaauuggaaugaguccac
uuuaaauccuuuaacgaggauccauuggagggcaagucuggugccagcag
ccgcgguaauuccagcuccaauagcguauauuaaaguugcugcaguuaaa
aagcucguaguuggaucuuuuuacuuugaaaaaauuagaguguucaaagc
aggcccgagccgccuggauaccgcagcuaggaauaauggaauaggaccgc
gguucuauuuuguugguuuucggaacugaggccaugauuaagagggacgg
ccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggcgc
aagacggaccagagcgaaagcauuugccaagaauguuuucauuaaucaag
aacgaaagucggagguucgaagacgaucagauaccgucguaguuccgacc
auaaacgaugccgaccggcgaugcggcggcguuauucccaugacccgccg
ggcagcuuccgggaaaccaaagucuuuggguuccggggggaguaugguug
caaagcugaaacuuaaaggaauugacggaagggcaccaccaggaguggag
ccugcggcuuaauuugacucaacacgggaaaccucacccggcccggacac
ggacaggauugacagauugauagcucuuucucgauuccgugggugguggu
gcauggccguucuuaguugguggagcgauuugucugguuaauuccgauaa
cgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcggucgg
cgucccccaacuucuuagagggacaaguggcguucagccacccgagauug
agcaauaacaggucugugaugcccuuagauguccggggcugcacgcgcgc
uacacugacuggcucagcgugugccuacccuacgccggcaggcgcgggua
acccguugaaccccauucgugauggggaucggggauugcaauuauucccc
augaacgaggaauucccaguaagugcgggucauaagcuugcguugauuaa
gucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugguu
uagugaggcccucggaucggccccgccgggcggagcgcugagaagacggu
cgaacuugacuaucuagaggaaguaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucauua
...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<<<<.........<<.....<<.<<<...
..>>>.>>......>>.........<<<<...<<<<<<....>>>>>>..
.>>>><<..<<<<<...<......>..>>>>>......>>...<<<<.<<
<<......>>>>>>>>.>>.>>>...>>..>.>>>.<<<....<<<....
<<<<<<<.........>>>>>>>>>>......>>>...<<<.<<<<....
>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<<....>>.>
...>>>>>>.........<<<....<<<<...>>>>..>>>..>...>>.
>.....<<<<<<<<<..<<....>>...>>>>>.>>>>......<<..<.
..........>..>>.........<<<<<((....<.<<<<.....<<..
))>>.......>>>>>>>>>>..>>>>>>.>>>.........<.<((...
..<.<<...<<<.<<.....<<<<<<.<.......<<...<.......>.
<<<<.......>>>>...>>......>.>>>..>>>........<.<<.<
<<.......................>>>.>>.>....>>....<<<<<<.
.<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>>>
>>..>>.......<<....>>...>>>>..>..>>>.>>>...>>>...>
>.>....<<<<<<<...<...<<<<.<.....>.>>>>...>>>>>>>>.
.........<<<.<<.<<<..<.<<<<<<.<<<<......>>>>>>>>>>
.>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<<.
...>>>>....>>>..)))).]<<<<<.<<<<<<<..<<..<<<<<..<<
<.<<<<<<......<<........>>..........<<<<<.<....<<<
<<<.......<<.<<<........>>>.>>.....>>>>>>...<<.<<<
..<<.<<<<<<....<<<.<<<<<....>>>...<<<......>>>...>
>.>>>....<<<...<...<<<<..<<<<<<<<<<<<.......>>>>.>
>>>.....>>>>..>>>>..>.....<<<<<.....>>>>>........>
>>....>>>.>>>.....>>>>>>>.....>.>>>>>...>>.>>>>.>>
>.....<<.<<<........<.......<<<.<<<<....>>>>.>>>..
..>.........>>>.>>......<.....<<<<<..........>>>>>
.....>.....>>>>>.....<<<<<<<<.......>>>>>>>>......
>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<<<<
.<<<..<<<<.<<...<<<<<.<<.......>>...>>>>>...>>.>>>
>..>>>.>>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<
....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB9bkd Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in the 40S small ribosomal subunit.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
Q4 S6 K7 K8 R9 R27 R117 K141 R143 Q145 R146 A147 K151 L156 M157 H159 S160 G161 D162 H174 R178 Q179 V181 G183 K185 P205 D206
Binding residue
(residue number reindexed from 1)
Q4 S6 K7 K8 R9 R27 R117 K141 R143 Q145 R146 A147 K151 L156 M157 H159 S160 G161 D162 H174 R178 Q179 V181 G183 K185 P205 D206
External links
PDB RCSB:9bkd, PDBe:9bkd, PDBj:9bkd
PDBsum9bkd
PubMed39117603
UniProtP23396|RS3_HUMAN Small ribosomal subunit protein uS3 (Gene Name=RPS3)

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