Structure of PDB 8rdv Chain aA Binding Site BS01

Receptor Information
>8rdv Chain aA (length=53) Species: 45610 (Psychrobacter urativorans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVQKSRKSRSRRDMRRSHHHMTVAELSVDATTGEKHRRHHMTKDGFYRGR
QLF
Ligand information
>8rdv Chain Z2 (length=2710) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gucaaguaaugaagcgcacaugguggaugccuuggcagucagaggcgaug
aaagacgugacagccugcgauaagcuucggggaggcggcaauauccugug
auccggagauuucugaauggggaaacccacuuaccauaagguagguaucu
uguacaagaagcgaacgaggggaagugaaacaucucaguacccuuaggaa
aagacaucaaaugagauuccccaaguagcggcgagcgaacggggagaagc
cgauuaaugcuaauguagaagaacagcgugggaaagcugaccguaguagg
ugauaguccuguauucgaaacauuagcguuaacauauuaaguagggcggg
acacgagaaauccugucugaagauggggggaccauccuccaaggcuaaau
acuccugacugaccgauagugaaccaguaccgugagggaaaggcgaaaag
aaccccugugaggggagugaaauagaaccugaaaccgugugcguacaagc
aguaggagccucaauuuauuggggugacugcguaccuuuuguauaauggg
ucagcgacuuauauucuguagcaagguuaaccguuuaggggagccguagg
gaaaccgagucuuaauagggcgucuaguugcaggguauagacccgaaacc
gagugaucuauccaugagcagguugaaagugccguaacaggcaccggagg
accgaacccacugucguugaaaagccaggggaugacuuguggauaggggu
gaaaggcuaaucaaacucggugacagcugguucuccccgaaagcuauuua
gguagcgccucggacgaauaccauuggggguagagcacuguuucggcacc
gaugcaaacuccgaauaccgaugaguaauauccgggagacacacggcggg
ugcuaacguccgucguggagagggaaacaacccagaccgccagcuaaggc
cccaaauuccuaguuaagugggaaacgaggugggaaggcauagacagcua
ggagguuggcuuagaagcagccauccuuuaaagaaagcguaauagcucac
uagucgagucggccugcgcggaagauguaacggggcucaaacuaggagcc
gaagcugcggauuugaaacuuguuuucaagugguaggggagcguugugua
agccugugaaggugugucguaaggcaugcuggagguaucacaagagcgaa
ugcugacgugaguaacgauaaugcgagugaaaagcucgcacgccggaaga
ucaaggguuccaguccaacguuaaucggggcugggugagucgaccccuaa
ggcgaggccgaaaggcguagucgaugggaaauugguuaauauuccaauac
uuguuuauagugcgauggagggacggagaagguuaugucagccuggcguu
gguuguccaggugaaaggauguaggcuuacaguuuaggcaaauccggacu
guaggcugagaucugauagcaaggaaguggcaaauaccaugcuuccagga
aaagcuucuaaggcuauaaacgaaucguacccuaaaccgacacaggugau
cagguagagaauaccaaggcgcuugagagaacucugcugaaggaacuagg
caaaaugguaccguaacuucgggagaagguacgcuguugauggugauagg
ucuccuugagcuuucgacagucgcagauaccaggcugcugcaacuguuua
uuaaaaacacagcacucugcaaacacgaaaguggacguauagggugugau
gccugcccggugcuggaagguuaauugaugggguuagcguaagcgaagcu
cuugaucgaagccccaguaaacggcggccguaacuauaacgguccuaagg
uagcgaaauuccuugucagguaaguucugaccugcacgaauggcauaaug
auggcagcgcugucuccagcagagacucagugaaaucgaaaucgcaguga
agaugcuguguacccgcggcuagacggaaagaccccgugaaccuuuacua
cagcuuuacauugaacuuggguucuaacucagguauaacaauaccgagga
caauguaugguggguaguuugacuggggcggucuccuccuaaagaguaac
ggaggaguacgaaggugcgcucagaacggucggaaaucguucauagagua
uaaaggcaaaagcgcgcuuaacugcgagacccacaagucgagcagguacg
aaaguaggucuuagugauccggugguucuguauggaagggccaucgcuca
acggauaaaagguacucuggggauaacaggcugauaccgcccaagaguuc
auaucgacggcgguguuuggcaccucgaugucggcucaucucauccuagg
gcugaagcagguccuaaggguauggcuguucgccauuuaaagagguacgc
gagcuggguuuagaacgucgugagacaguucggucccuaucuaccguggg
cguuggaaauuugagaggaucugcuccuaguacgagaggaccagagugga
cgaaccucugguguucggguugucacgccaguggcauugcccgguagcua
cguucggaugggauaaccgcugaaagcaucuaagcgggaagcccaccuca
agauuagauuucccuaaagagccguugaagacuacgacguugauaggcag
gguguggaagugcagcgaugcauguagcuaaccuguacuaauugcucguu
uggcuugacc
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<<..>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>...
......<<....>>..<<<<<<.....<<.....>>....>>>>>>..<<
<..<<<<<<<<<<<<<.<<<...<<<<........>>>>((......<<<
.....))>>>...>>>...>>>>>>>>>>>>>...........<<<<<<<
<.........>>>>>>>>......<<<<<..((((>>>>>..>>>.....
.>>.>>>>>>>.>>>..............<<....>>....>>.......
..<<<<.....>>>>..................>>>>>>>>>>>......
.<<<<..<<<<<<<....>>>>>>>..>>>>...<............>.<
<<<<<....<<<<<<<<<<<<<..<<<...<<.....>>...>>>...<<
....>>..<<<<.....>>>>.....>>>>>>>>>>>>>..<<.<...<<
<<<<.....<<<<<<<<<..<<<<....<<<<<......>>>>>..>...
>>>...<<<.<<<.<........>.>>>>>>....>>>>>>>>>...<<<
.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<...
.>>>>>.<<<<<<<....<<<<<<<<<.....<<<...<<<.<<<<..>>
>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>.>...<<<<<<<<<
<......>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<
(((.....<<<<<<...........<<..<<<<<..<<........<<<<
<.<<<..<<<<.......>>>>..>>>........<<<......>>>..>
>>>>....>>..>>>>>.>>...........)))......>>>>>>.>>>
...>>>>>>><<<<<<.<.....>.>>>>>>....>>>>>>..<<<<<..
.<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.......
.>>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...
<<<...<<<....>>>...>>>...>>>..<<<<<........>>>>>))
<<<<<<<<<<<.<...<<<<....<<<<..<<<..<<<<<<<<<<<...[
[[[...>>>>>>....<<<<...<<<<<<<<<<<..<<.....>>.>>>>
>>>>>>>...>>>>.............>>>>>...>>>...>>>>.....
....>>>>...>>>>>>>>>>>>.>>>..>>.....<<......>>>>>>
>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<........
.......<<<<<...............>>>>><<<<<<<<.<<<...<<<
...>>>...>>>.>>>>>>>>............<<<<<<<<<..<<<...
......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<
<<<.<<<..<<<<<<<..<<<....<...<<<<<<.<<....>>..>>>>
>>..>.....>>>>>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<<.....>>>>>>.....>....>>>>>..>>
.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>.....<<<<<...
.....>>>>>..<<<<<<<.<<<<.<<......<<<<.<<<<<<..<<<<
<.<<<.<<<<<.<<<<<..>>>>>...<<<.<<<<<....>>>>>>>>..
..>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<.
...>>>.>>)))]......<<<<<<<.<<..))))..>>>>>>>>>....
.........>>>>..>>>>>>.......<<<<...<<<<<<...<<....
...>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<<<
<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>.
..>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>>>>>>>>>
....<<<<<<<...<<<<..<<<<<<.................>>>>>>.
<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>..>>>>>...>>>>
.>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>>.
......>>>>>>>.....<<<<<<<<<.......>>>>>....<<<<<<<
<..<<....<<<<<....>>>>>...>>...>>>>>.>>>...>>>>...
..>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8rdv A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis
Resolution2.6 Å
Binding residue
(original residue number in PDB)
A2 V3 Q4 K5 S6 R7 K8 S9 R10 S11 R12 R13 D14 M15 R16 R17 S18 H19 E26 R39 H40 Y48 R49
Binding residue
(residue number reindexed from 1)
A1 V2 Q3 K4 S5 R6 K7 S8 R9 S10 R11 R12 D13 M14 R15 R16 S17 H18 E25 R38 H39 Y47 R48
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8rdv, PDBe:8rdv, PDBj:8rdv
PDBsum8rdv
PubMed38355796
UniProtA0A0M4SWQ6

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