Structure of PDB 6ogi Chain U Binding Site BS01

Receptor Information
>6ogi Chain U (length=82) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGT
RLDLDRIAHWVGQGATISDRVAALIKEVNKAA
Ligand information
>6ogi Chain 3 (length=1539) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuu
cgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaac
aagguaaccguaggggaaccugcgguuggaucaccuccu
.......<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....
<<<.<<<..<<<..<<.<...<<<.<<<<<......>>>>>..>>>.>..
>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<....
..<<<<......>>>>.......>>.>.....<<<....>>>....<<<<
<.<.<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<..
<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....>
>>>...>>>>.>>.<<<<.<<.........>>>>>>.<<<<....>>>>.
..>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>>
>>..<<<<......<<<<....>>>>.....>>>>..<<.<<<<<.....
.<.<<<<<<<<.<...>.>>>>>>>>..>.......>>>>>....>>.<<
<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>>
>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<<
<<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>.
>..<<<<<<<<...<<<<<<<.....<<<.<<....<<<......>>>..
.....>.>>>>............<<....>>.>>>>>>>..>>>.>>>>>
...>>>...>>>>....<<<<<<...<<...<<<<.........>>>>..
.>>>>>>>>..........<<<<<<..<<<<.<<<<<<<.....>>>>>>
>.>>>>...<<..))>>.....>>>>>>.>>>.<<<......<<<<....
>>>>....>>>..)))).]<<<<<.<<<<<<<.<..<<<<<...<<<<<<
<..<......<<........>>..........<<<<<<........<..<
<<..<<.<.<<....>>..>>>...<<....>>..>>>...>...<..<<
<..<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>..
>>>>>>.....<<<..<<<<<<....<...<<<.....>>>.>.....>>
>>>>.....<<<<<.....>>>>>.........>>>.........>>>..
.>>>>>>>......>>>>>>...>...>>>>>>>.....<<<<<<<....
.<<<..<<...<<<....>>>...>>....>>>.....>>>>>>>.....
......<<<<..............>>>>...........>>>>>....<<
<<<<...........>>>>>>.......>...>>>>>>>>>>.>>....<
..<<...<<<<.<<<..<<<<<<<<<<<<....<<<<...<<<...<<..
..>>..>>>..>>>>...>>>>>>>>>>>>..>>>.>>>>....>>...>
.....<<<<<<<<<....>>>>>>>>>............
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6ogi Extensive ribosome and RF2 rearrangements during translation termination.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		M1 V2 R5 L6 R8 G10 A11 K12 K13 R14 F16 Y17 D23 R25 R28 N29 G30 R31 F38 K46 Q63 G64 S68 R70 K76 E77
Binding residue
(residue number reindexed from 1)		M1 V2 R5 L6 R8 G10 A11 K12 K13 R14 F16 Y17 D23 R25 R28 N29 G30 R31 F38 K46 Q63 G64 S68 R70 K76 E77
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000400 four-way junction DNA binding
GO:0003735 structural constituent of ribosome
GO:0004519 endonuclease activity
GO:0004520 DNA endonuclease activity
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006259 DNA metabolic process
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:6ogi, PDBe:6ogi, PDBj:6ogi
PDBsum6ogi
PubMed31513010
UniProtP0A7T3|RS16_ECOLI Small ribosomal subunit protein bS16 (Gene Name=rpsP)

[Back to BioLiP]