Structure of PDB 6b4v Chain BC Binding Site BS01

Receptor Information

>6b4v Chain BC (length=84) Species: 262724 (Thermus thermophilus HB27)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPLA

Ligand information

>6b4v Chain FB (length=2880)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccauc
cuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaa
ugaucggggcucaagcccagcgccgaagcugcgggucugggggaugaccc
caggcgguaggggagcguucccgaugccgaugaaggccgacccgcgaggg
cggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagag
ggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucgu
cagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaa
gggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacg
cucuaggcuagggggaccggagccauggacgagcccggccagaagcgcag
ggugggagguaggcaaauccgccucccaaaagcucugcgugguggggaag
cccguacgggugacaaccccccgaagccagggagccaagaaaagccucua
agcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggug
caagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaagu
uggccccguaacuucgggagaaggggugcucccuggggugaugagcuccg
gggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcuc
ucugcgaacucguaagaggagguauagggagcgacgcuugcccggugccg
gaaggucaaggggaggggugcaagccccgaaccgaagccccggugaacgg
cggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaag
uuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggg
acccggugaaauugaacuggccgugaagaugcggccuacccguggcagga
cgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucg
cgccugcguaggauaggugggagccugugaacccccgccuccgggugggg
gggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccuc
ggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccucc
uaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaaucc
gccggagagcgcaaggguagaagggggccugacugcgaggccugcaagcc
gagcaggggcgaaagccgggccuagugaaccgguggucccguguggaagg
gccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucucc
cccgagcguccacagcggcggggagguuuggcaccucgaugucggcucgu
cgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauua
aagcggcacgcgagcuggguucagaacgucgugagacaguucggucucua
uccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagagg
accggaagggacgcaccucugguuucccagcugucccuccaggggcauaa
gcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcggg
aagcccgccccaagaugaggccucccacggcgucaagccgguaaggaccc
gggaagacgacccgguggaugggccggggguguaagcgccgcgaggcguu
gagccgaccggucccaaucguccgaggucu

<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<.
.......>>>>>.>>....<<<<<.....<<....>>......>>>>>..
.........<<....>>...<<<<<.....<<.....>>....>>>>>..
.<<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<
<...<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<..
...))>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<
<<<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>
......>>.>>>>>>.>>...............<<....>>....>>...
......<<<<....>>>>..................>>>>>>>>>>>...
....<<<<<<<<<<<....>>>>>>>>>>>...<.<........>.>.<<
<<<<....<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<
<....>>..<<<<.....>>>>.....>>>>>>>>>>>>>..<<.<...<
<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>>>....
.>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>...<<
<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<..
..>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<...
<<<<.<......>.>>.>>...>>>>>>>>..>>.>...>>>>>>>>>..
...>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<.
.....>>>...<<<<.<<<...<<<(((.....<<<<<<...........
<<..<<<<<<<<<........<<<<<..<.....................
>..........<........>...>>>>>....>>>>>>>>>.>>.....
.....)))......>>>>>>.>>>...>>>>>>><<<<<<<<.....>>>
>>>>>....>>>>>>..<<<<<...<<<......<<<<<.<<<....>>>
>>>>>...>>>..>>>>>........>>>>>><......<<.....<<<<
<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....
>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...
>>...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....<
<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<<...<<<<<<
<<<<<<<<<<.<<.....>>>>>>>>>....>>>>>>>>>..>>><...<
<<<<..>>>>>.....>>>>>>...>>>..>>>>>.........>>>>..
.>>...>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<
<....>>>>>..>>>>..<<<<....<<<<<<<<.<<.........<...
..<<<<<.....<..>......>>>>><<<<<<<<<<<<.....>>>>>>
>>>>>>............<<<<<<<<<..<<<.........>>>..<<<<
<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<
<..<<<...<<...<<<<<....>>>>>...>>...>>>>>>>>..>>>>
><<<<<<.......>>>>>>........<...........<<<<<<....
.>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>
.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.<<<
.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<.<<<<<
<<<<...........<<<<...<<<.......<<<<<<......>>>>>>
....>>>.............>>>>..>>>>>>>>>.>>>>>>...<<<<<
....>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<
...........>>>>>>..<<...<<<<<<<...<<<<<<.......>>>
>>>.....<<...(((>>....>>>>>>>...<<<<..<<<......>>>
..>>>>.<<<....>>>.>>))).......<<<<<<<.<<..))))..>>
>>>>>>>.............>>>>..>>>>>>.......<<<<...<<<<
<<...<<.......>>...>>>>>>....>>>.>.......<<<<<.<<<
<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>...
..>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>........
>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<............
...>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>...
>>>>>...>>>>.>>>>>...<<<....<<<<<...........>>>>>.
...>>>.>>>>.......>>>>>>>...<<<.....>>>.....<<<<<<
<<<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>.
..>>>..>>>>>.>>>...>>>>....>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6b4v Mechanism of Inhibition of Translation Termination by Blasticidin S.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): H3 K4 K5 S9 T10 R11 N12 R14 D15 S16 Q17 A18 K19 R20 K24 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 R44 G54 R55 D56 F57 F60 L62 F69 R74 R77
• Binding residue (residue number reindexed from 1): H2 K3 K4 S8 T9 R10 N11 R13 D14 S15 Q16 A17 K18 R19 K23 Y25 E26 Q28 R31 A32 G33 N34 I35 R38 R40 G41 T42 R43 G53 R54 D55 F56 F59 L61 F68 R73 R76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6b4v, PDBe:6b4v, PDBj:6b4v
• PDBsum: 6b4v
• PubMed: 29366636
• UniProt: Q72HR3|RL27_THET2 Large ribosomal subunit protein bL27 (Gene Name=rpmA)