Structure of PDB 5v8i Chain 1E Binding Site BS01

Receptor Information

>5v8i Chain 1E (length=204) Species: 262724 (Thermus thermophilus HB27)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

Ligand information

>5v8i Chain 1A (length=2862)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgucuaguccgcggccguggacccgaaaccgggcgagcu
agcccuggccagggugaagcuggggugagacccaguggaggcccgaaccg
gugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcua
accgagcccggagauagcugguucuccccgaaaugacuuuagggucagcc
ucaggcgcugacuggggccuguagagcacugauagggcuagggggcccac
cagccuaccaaacccugucaaacuccgaagggucccagguggagccuggg
agugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgag
accgccagcuaaggcccccaagucugggcuaagugguaaaggauguggcg
ccgcgaagacagccaggagguuggcuuagaagcagccauccuuuaaagag
ugcguaauagcucacuggucgaguggcgccgcgccgaaaaugaucggggc
ucaagcccagcgccgaagcugcgggucugggggaugaccccaggcgguag
gggagcguucccgaugccgaugaaggccgacccgcgagggcggcuggagg
uaagggaagugcgaaugccggcaugaguaacgauaaagagggugagaauc
ccucucgccguaagcccaaggguuccuacgcaauggucgucagcguaggg
uuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgg
uuaauauuccggcccuucccgcaggugcgauggggggacgcucuaggcua
gggggaccggagccauggacgagcccggccagaagcgcagggugggaggu
aggcaaauccgccucccaaaagcucugcgugguggggaagcccgggugac
aaccccccgaagccagggagccaagaaaagccucuaagcacaaccugcgg
gaacccguaccgcaaaccgacacaggugggcgggugcaagagcacucagg
cgcgcgggagaacccucgccaaggaacucugcaaguuggccccguaacuu
cgggagaaggggugcucccuggggugaugagcuccggggagccgcaguga
acaggcucuggcgacuguuuaccaaaaacacagcucucugcgaacucgua
agaggagguauagggagcgacgcuugcccggugccggaaggucaagggga
ggggugcaagccccgaaccgaagccccggugaacggcggccguaacuaua
acgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacg
aaaagcguaacgaccggagcgcugucucggcgagggacccggugaaauug
aacuggccgugaagaugcggccuacccguggcaggacgaaaagaccccgu
ggagcuuuacugcagccugguguuggcucuuggucgcgccugcguaggau
aggugggagccugugaacccccgccuccgggugggggggaggcgccggug
aaauaccacccuggcgcggcugggggccuaacccucggauggggggacag
cgcuuggcgggcaguuugacuggggcggucgccuccuaaaagguaacgga
ggcgcccaaagguccccucaggcgggacggaaauccgccggagagcgcaa
ggguagaagggggccugacugcgaggccugcaagccgagcaggggcgaaa
gccgggccuagugaaccgguggucccguguggaagggccaucgaucaacg
gauaaaaguuaccccggggauaacaggcugaucucccccgagcguccaca
gcggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcu
gaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgag
cuggguucagaacgucgugagacaguucggucucuauccgccacgggcgc
aggaggcuugaggggggcucuuccuaguacgagaggaccggaagggacgc
accucugguuucccagcugucccuccaggggcauaagcuggguagccaug
ugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgccccaag
augaggccucccacggcagccgguaaggacccgggaagacgacccggugg
augggccggggguguaagcgccgcgaggcguugagccgaccggucccaau
cguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v8i Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17
• Resolution: 3.25 Å
• Binding residue (original residue number in PDB): K8 M11 T12 R13 P22 R37 K41 D42 Y44 Q48 R58 N60 R61 P62 L63 H66 K69 R76 R79 E80 R82 K109 G110 R111 G112 F113 G115 M117 K118 R119 F122 A123 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 G153 K154 M156 A157 H159 Y160 R164 V165 T166 M168 N169 L170 G186 A187 V188 P189 G190 P191 N192 K202 K203
• Binding residue (residue number reindexed from 1): K8 M11 T12 R13 P22 R37 K41 D42 Y44 Q48 R58 N60 R61 P62 L63 H66 K69 R76 R79 E80 R82 K109 G110 R111 G112 F113 G115 M117 K118 R119 F122 A123 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 G153 K154 M156 A157 H159 Y160 R164 V165 T166 M168 N169 L170 G186 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:5v8i, PDBe:5v8i, PDBj:5v8i
• PDBsum: 5v8i
• UniProt: Q72I04|RL3_THET2 Large ribosomal subunit protein uL3 (Gene Name=rplC)