Structure of PDB 1ond Chain Z Binding Site BS01

Receptor Information
>1ond Chain Z (length=58) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGY
YDGRQVLA
Ligand information
>1ond Chain 0 (length=2765) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaau
ucaaccccucaagccgaaguggcuggaaagcuacaccucagaaggugaga
guccuguaggcgaacgagcgguugacuguaaggucguuguucgugaaacg
augacugaauccgcgcggaccaccgcgcaaggcuaaauacucccagugac
cgauagcgcauaguaccgugagggaaaggugaaaagaaccccgggagggg
agugaaagagaaccugaaaccguggacuuacaagcagucauggcaccuua
ugcguguuauggcgugccuauugaagcaugagccggcgacuuagaccuga
cgugcgagcuuaaguugaaaaacggaggcggagcgaaagcgaguccgaau
agggcggcauuaguacgucgggcuagacucgaaaccaggugagcuaagca
ugaccagguugaaacccccgugacagggggcggaggaccgaaccggugcc
ugcugaaacagucucggaugaguuguguuuaggagugaaaagcuaaccga
accuggagauagcuaguucuccccgaaauguauugagguacagccucgga
uguugaccauguccuguagagcacucacaaggcuaaaaccuuaugaaacu
ccgaaggggcacgcguuuaguccgggagugaggcugcgagagcuaacuuc
cguagccgagagggaaacaacccagaccaucagcuaaggucccuaaauga
ucgcucagugguuaaggaugugucgucgcauagacagccaggagguuggc
uuagaagcagccacccuucaaagagugcguaauagcucacuggucgagug
acgaugcgccgaaaaugaucggggcucaagugaucuaccgaagcuaugga
uucaacucgcgaagcgaguugucugguaggggagcguucaguccgcggag
aagccauaccggaaggagugguggagccgacugaagugcggaugccggca
ugaguaacgauaaaagaagugagaaucuucuucgccguaaggacaagggu
uccuggggaagggucguccgcccagggaaagucgggaccuaaggugaggc
cgaacggcgcagccgauggacagcaggucaagauuccugcaccgaucaug
uggagugauggagggacgcauuacgcuauccaaugccaagcuauggcuau
gcugguugguacgcucaagggcgaucgggucagaaaaucuaccggucaca
ugccucagacguaucgggagcuuccucgaagcgaaguuggaaacgcgacg
gugccaagaaaagcuucuaaacguugaaacaugauugcccguaccgcaaa
ccgacacagguguccgagugucaaugcacuaaggcgcgcgagagaacccu
cguuaaggaacuuugcaaucucaccccguaacuucggaagaagggguccc
cacgcuucgcguggggcgcagugaauaggcccaggcgacuguuuaccaaa
aucacagcacucugccaacacgaacaguggacguauagggugugacgccu
gcccggugccggaaggucaaguggagcggugcaagcugcgaaaugaagcc
ccggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaaaggcguaacgaucugggcgcugu
cucaacgagggacucggugaaauugaauuggcuguaaagaugcggccuac
ccguagcaggacgaaaagaccccguggagcuuuacuauagucuggcauug
ggauucggguuucucugcguaggugggagaaacuggccggucgguggcca
cccugagaaacuuggauuucuaaccugaaaaaucacuuucggggaccgug
cuuggcggguaguuugacuggggcggucgccucccaaaauguaacggagg
cgcccaaaggucaccucaagacgguuggaaaucgucuguagagcgcaaag
guagaagguggcuugacugcgagacugacacgucgagcagggaggaaacu
cgggcuuagugaaccggugguaccguguggaagggccaucgaucaacgga
uaaaaguuaccccggggauaacaggcugaucucccccgagaguccauauc
ggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcuga
agaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcu
ggguucagaacgucgugagacaguucggucucuauccgcuacgggcgcag
gagaauugaggggaguugcuccuaguacgagaggaccggagugaacggac
cgcuggucucccugcugucguaccaacggcacaugcaggguagcuauguc
cggaacggauaaccgcugaaagcaucuaagcgggaagccagccccaagau
gaguucucccacuguucagguaagacucccggaagaccaccggguuaaga
ggccaggcgugcacgcauagcaauguguucagcggacuggugcucaucag
ucgaggucuugacca
<<<<<<<<......<<<<<<<<<<<.....<<.<<<<<<<<<<<<<....
..<<<<<<<((..((>>>>.....<<<<<<...<<.))..))..>>....
..>>>>>>...>>>....<<<....>>><<<<<....>>>>>.<<<....
>>>.>>...<<<<<<.....<<....>>......>>>>>.>.........
<<....>>...<<<<......<<.....>>.....>>>>...<<<.....
<<<<<<.<<<..<<<...<<<<<......>>>>>((......<<<.....
))>>>...>>>....>>>.>>>>>>......<<<<<<<<<.......>>>
>>>>>>......<<<<<..((((>>>>>..>>>......>>.>>>>>>.>
>>.............<<....>>....>>.........<<<<....>>>>
..................>>>>>>>>>>>.......<<<<<<<<<<....
...>>>>>>>>>>...<.<........>.>.<<<<<<....<<<.<<<<<
<<<<<...<<...<<......>>...>>....<<....>>...<<.....
.>>.........>>>>>>>>>>>>>..<<.<..<<<<<<<....<<<<<<
<<<<..<<<.....<<<<<......>>>>>......>>>...<<<..<.<
<<......>>>.>.>>>....>>>>>>>>>>..<<<.....>>>......
>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<
<...<<<<.<<<<<....<<....<<<.<<<<.<..>.>>>>.>>>...>
.>....>>>>>.>.>>>..>>>>>>>.>>..<<<<<<<.<<......>>.
>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<
<<<<...........<<..<<<<<<<<..........<<<..<<<...<<
.........>>...>>>.........<<......>>....>>>......>
>>>>>>>.>>..........)))......>>>>>>.>>>...>>>>>>>.
.<.<<<<<<.....>>>>>>>.......>>>>>>..<<<<<<<.<<....
..<<<<<.<<....>>.>>>>>...>>.>>>>>>>........>>>>>><
......<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<..
.<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<
<<..>>>>...>>>...>>...<<<<<........>>>>>))<<<<<<<<
<...<<...<<<<....<<<<..<<<..<<<<<.<<<<.<<...[[....
>>>>>>.<.<<<<.<<.<<<..<<<<<<.............>>>>>>...
..>>>..>>>>>>>.....<<<<<...>>>>>....>>>>>...>>>...
>>>>.........>>>>...>>......>>>>>>>>>>>>>..>>.....
<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<....<<<<
<<<<.<<.........<.....<<<<<...............>>>>><<<
<<<<<...>>>>>>>>............<<<<<<<<<..<<.........
..>>..<<<<<<<.....<<<.....>>>.......>>>>>>>.<<<<<.
<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>
>>>>>..>>>>><<<<<<.......>>>>>>........<..........
.<<<<<.......>>>>>.....>....>>>>>..>>.>>>>>>>..>..
>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<
<<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<..<
<<<<<..<<<.<<<<.<....<<<<<.....<<<<<<..>>>>>>..>>>
>>>.>>>>.>>>..>>>>>>...<<<<<<........>>>>>>.....>>
>>.>>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>
>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<....(((
.>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>
>.>>))).......<<<<<<<.<<..))))..>>>>>>>>>.........
....>>>>..>>>>>>.......<<<<.<<<<<<<<.<.<<.......>>
..>>>>>>>>..>>>>.>.......<<<<<..<<<<<..<<<<<<<<<..
....>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>......>>>
.>>....<<<<<<<....>>>.>>>>........>>>>>>>>>>>....<
<<<<<<...<<<<..<<<<<<<...............>>>>>>>.<<<<<
....<<<...<<<<<<<<<<<.]].>>>>>>...>>>>>...>>>..>>>
>>....<<....<<<<.............>>>>....>>..>>>>.....
..>>>>>>>..<<<..>>>....<<<<<<<<<.......>>>>>....<<
<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>
>>....>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1ond Structural insight into the role of the ribosomal tunnel in cellular regulation
Resolution3.4 Å
Binding residue
(original residue number in PDB)		K3 H4 P7 K10 S14 S21 H43
Binding residue
(residue number reindexed from 1)		K2 H3 P6 K9 S13 S20 H42
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015934 large 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:1ond, PDBe:1ond, PDBj:1ond
PDBsum1ond
PubMed12665853
UniProtP49228|RL32_DEIRA Large ribosomal subunit protein bL32 (Gene Name=rpmF)

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