Structure of PDB 6gsk Chain 21 Binding Site BS01

Receptor Information

>6gsk Chain 21 (length=205) Species: 300852 (Thermus thermophilus HB8)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKAA

Ligand information

>6gsk Chain 1H (length=2811)

uaagggcccacgguggaugccucggcacccgagccgaugaaggacguggc
uaccugcgauaagccagggggagccgguagcgggcguggaucccuggaug
uccgaaugggggaacccggccggcgggaacgccggucaccgcgcuuuuug
cgcggggggaaccuggggaacugaaacaucucaguacccagaggagagga
aagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccuaa
accguccggcuuguccgggcggggucguggggcccucggacaccgaaucc
ccagccuagccgaagcuguugggaagcagcgccagagagggugaaagccc
cguaggcgaaagguggggggauaggugaggguacccgaguaccccguggu
ucguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguac
uccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaac
cccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguc
acggccccgcaagggguuguggcgugccuauugaagcaugagccggcgac
ucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaacc
gaguccgaacagggcgcaaacgggggccgaaaaguccgcggccguggacc
cgaaaccgggcgagcuagcccuggccagggugaagcuggggugagaccca
guggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggc
uaggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaau
gacuuuagggucagccucaggcgcugacuggggccuguagagcacugaua
gggcuaggccucaaacccugucaaacuccgaagggucccagguggagccu
gggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaacc
gagaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugug
gcgccgcgaagacagccaggaaaugccucacuggucgaguggcgccgcgc
cgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucuggggga
ugaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccg
cgagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgau
aaagagggugagaaucccucucgccguaagcccaaggguuccuacgcaau
ggucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcgua
gccgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggg
gggacgcucuaggcuagggggaccggagccauggacgagcccggccagaa
gcgcagggugggagguaggcaaauccgccucccaacaagcucugcguggu
ggggaagcccguacgggugacaaccccccgaagccagggagccaagaaaa
gccucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugg
gcgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacuc
ugcaaguuggccccguaacuucgggagaaggggugcucccuggggugaug
agccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaac
acagcucucugcgaacucguaagaggagguauagggagcgacgcuugccc
ggugccggaaggucaaggggaggggugcaagccccgaaccgaagccccgg
ugaacggcggccguaacuauaacgguccuaagguagcgaaauuccuuguc
ggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucg
gcgagggacccggugaaauugaacuggccgugaagaugcggccuacccgu
ggcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcuc
uuggucgcgccugcguaggauaggugggagccuaacccccgccuccgggu
ggggggggcgccggugaaauaccacccuggcgcggcugggggccuaaccc
ucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccu
ccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaau
ccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaag
ccgagcaggggcgaaagccgggccuagugaaccgguggucccguguggaa
gggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucu
cccccgagcguccacagcggcggggagguuuggcaccucgaugucggcuc
gucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccau
uaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccuccguaaggacccgggaagaccaccc
gguggaugggccggggguguaagcgccgcgaggcguugagccgaccgguc
ccaaucguccg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gsk Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria.
• Resolution: 3.36 Å
• Binding residue (original residue number in PDB): K8 M11 T12 R13 P22 Q35 R37 D42 Y44 R58 N60 R61 P62 L63 H66 K69 L78 R79 E80 R82 S108 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 G158 H159 R164 V165 T166 M168 K185 A187 V188 P189 G190 P191 N192 K202 K203
• Binding residue (residue number reindexed from 1): K8 M11 T12 R13 P22 Q35 R37 D42 Y44 R58 N60 R61 P62 L63 H66 K69 L78 R79 E80 R82 S108 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 G158 H159 R164 V165 T166 M168 K185 A187 V188 P189 G190 P191 N192 K202 K203

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:6gsk, PDBe:6gsk, PDBj:6gsk
• PDBsum: 6gsk
• PubMed: 29931292
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)