Structure of PDB 6b4v Chain F Binding Site BS01

Receptor Information

>6b4v Chain F (length=204) Species: 262724 (Thermus thermophilus HB27)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

Ligand information

>6b4v Chain B (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): K8 M11 T12 R13 P22 Q35 R37 K41 Y44 Q48 R58 N60 R61 P62 G65 H66 K69 R76 L78 R79 E80 R82 K109 G110 R111 G112 F113 A114 G115 K118 F122 D127 S128 H129 G130 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 Y160 R164 T166 M168 N169 L170 K185 G186 A187 V188 P189 G190 P191 K202 K203 A204
• Binding residue (residue number reindexed from 1): K8 M11 T12 R13 P22 Q35 R37 K41 Y44 Q48 R58 N60 R61 P62 G65 H66 K69 R76 L78 R79 E80 R82 K109 G110 R111 G112 F113 A114 G115 K118 F122 D127 S128 H129 G130 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 Y160 R164 T166 M168 N169 L170 K185 G186 A187 V188 P189 G190 P191 K202 K203 A204

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

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: Q72I04|RL3_THET2 Large ribosomal subunit protein uL3 (Gene Name=rplC)