Structure of PDB 9bkd Chain B Binding Site BS01

Receptor Information
>9bkd Chain B (length=143) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIQTERAYQKQPTIFQNKKRKEKLPRYYKNIGLGFKTPKEAIEGTYIDKK
CPFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNM
SVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAGTK
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)		E7 R8 Q11 P14 T15 F17 Y36 N39 I40 G41 L42 K58 K59 N65 S67 R69 R71 K79 K81 M82 Q83 T85 V87 R89 R90 Y92 H94 K98 K104 R105 H106 K107 N108 E130 R132 P133 L134 S135 K136 T137 R139 F140 K152
Binding residue
(residue number reindexed from 1)		E5 R6 Q9 P12 T13 F15 Y27 N30 I31 G32 L33 K49 K50 N56 S58 R60 R62 K70 K72 M73 Q74 T76 V78 R80 R81 Y83 H85 K89 K95 R96 H97 K98 N99 E121 R123 P124 L125 S126 K127 T128 R130 F131 K143
External links
PDB RCSB:9bkd, PDBe:9bkd, PDBj:9bkd
PDBsum9bkd
PubMed39117603
UniProtP62280|RS11_HUMAN Small ribosomal subunit protein uS17 (Gene Name=RPS11)

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