Structure of PDB 8rd8 Chain SP Binding Site BS01

Receptor Information
>8rd8 Chain SP (length=80) Species: 45610 (Psychrobacter urativorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRSLKKGPFIDAHLFAKVENALETNSRKPIKTWSRRSMILPQMVGLTLSV
HNGRTHVPVIVSEQMVGHKLGEFAPTRTYR
Ligand information
>8rd8 Chain iN (length=1503) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aaacugaagaguuugaucauggcucagauugaacgcuggcggcaggcuua
acacaugcaagucgagcgguaacaggagaagcuugcuucuugcugacgag
cggcggacgggugaguaauacuuaggaaucuaccuaguagugggggauag
cucggggaaacucgaauuaauaccgcauacgaccuacgggagaaaggggg
cucucgcuauuagaugagccuaagucggauuagcuagauggugggguaaa
ggccuaccauggcgacgaucuguagcuggucugagaggaugaucagccac
accgggacugagacacggcccggacuccuacgggaggcagcaguggggaa
uauuggacaaugggggcaacccugauccagccaugccgcgugugugaaga
aggccuuuugguuguaaagcacuuuaagcagugaagaagacuccgugguu
aauacccacggacgaugacauuagcugcagaauaagcaccggcuaacucu
gugccagcagccgcgguaauacagagggugcaagcguuaaucggaauuac
ugggcguaaagggagcguagguggcucgauaagucagaugugaaaucccc
gggcuuaaccugggaacugcaucugauacuguugagcuagaguaugugag
aggaagguagaauuccagguguagcggugaaaugcguagagaucuggagg
aauaccgauggcgaaggcagccuucuggcauaauacugacacugaggcuc
gaaagcguggguagcaaacaggauuagauacccugguaguccacgccgua
aacgaugucuacuagucguuggguccggacuuagugacgcagcuaacgca
auaaguagaccgccuggggaguacggccgcaagguuaaaacucaaaugaa
uugacgggggcccgcacaagcgguggagcauguuguuuaauucgaugcaa
cgcgaagaaccuuaccuggucuugacauaucuagaauccugcagagaugc
gggagugccuucgggaauuagaauacaggugcugcauggcugucgucagc
ucgugucgugagauguuggguuaagucccgcaacgagcgcaacccuuguc
cuuaguuaccagggaacucuaaggauacugccagugacaaacuggaggaa
ggcggggacgacgucaagucaucauggcccuuacgaccagggcuacacac
gugcuacaaugguagguacagagggcagcuacacagcgaugugaugcgaa
ucucaaaaagccuaucguaguccggauuggagucugcaacucgacuccau
gaaguaggaaucgcuaguaaucgcggaucagaaugccgcggugaauacgu
ucccgggccuuguacacaccgcccgucacaccaugggaguugauugcacc
agaaguggauagcuuaaccuucgggaaggcguucaccacggugugguuga
ugacuggggugaagucguaacaagguagccguaggggaaccugcggcugg
auc
........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<<..<<<<<<..........>>>.>>>>>..>
>>>>......<<.......<<<<<<<..<<...<<<<<<<<<.<<....<
.<<<<<....>>>>>.>.....>>.>......<<....>>.....<<<<.
.>>>>>>>>>>>>..>>.>>>>>>><<<....<<<..<<<<<<<<.....
..>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>
.<<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>.....
....<<<...<<<<<....>>>>.>>>>..>>.>>>>>>..<<<<.....
.<<<<....>>>>.....>>>>...<.<<<<<.........<<<<<<<..
.....>>>>>>>...........>>>>>....>..<<<<<(((...<<<<
<.....<<.)))>>.......>>>>>>>>>>..>>>>>>>>>........
..<<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<
<<<.....>>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<..
.<<<<<<<....<<<<<<<<...<<<......>>>......>>>>>>>>.
..........<<....>>.>>>>>>>..>>>.>>>>>...>>>...>>>>
....<<<<<<...<<...<<<<.<.....>.>>>>...>>>>>>>>....
......<<<<<<..<<<<<<<<<<<<>>>>>>>>>>>>...<<..))>>.
....>>>>>>.>>>.<<<......<<<<....>>>>....>>>..)))).
]<<<<<.<<<<<<<.<<.<<<<<<..<<<<<<<.<<......<<......
..>>..........<<<<<<<......<<<<<<<..<<<<<<<....>>>
>>>>...<<<..>>>..>>>>>.>>.<<<.<<<..<<<<<<.......<<
<<<<<<<....>>>..<<<<......>>>>..>>>>>>.....<<<<<<<
<<<<<...<<..>>....>>>>>>>>....<<<<<.....>>>>>.....
...>>>>.........>>>...>>>>>>>>>...>>>>>>>...>>..>>
>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>..>>...
.>>>.....>>>>>>>......<....<<<<<<<........>>>>>>>.
...>.....>>>>>>....<<<<<<<.........>>>>>>>......>>
...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<<<<
....<<<<<<.<<<<..<<....>>.>>>>>>>>>>...>>>>>>>>>>>
>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>>..
...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8rd8 A new family of bacterial ribosome hibernation factors
Resolution2.62 Å
Binding residue
(original residue number in PDB)		P2 R3 S4 L5 K6 K7 F10 H14 W34 R36 R37 H52 G54 R55 K70 G72 E73 T77 R78 Y80
Binding residue
(residue number reindexed from 1)		P1 R2 S3 L4 K5 K6 F9 H13 W33 R35 R36 H51 G53 R54 K69 G71 E72 T76 R77 Y79
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8rd8, PDBe:8rd8, PDBj:8rd8
PDBsum8rd8
PubMed38355796
UniProtA0A0M4TUJ8

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