Structure of PDB 4v4j Chain C Binding Site BS01

Receptor Information

>4v4j Chain C (length=201) Species: 262724 (Thermus thermophilus HB27)

GILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFL
PQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERV
DVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYK
GKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRETK
K

Ligand information

>4v4j Chain w (length=2889)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgucuaguccgcggccguggacccg
aaaccgggcgagcuagcccuggccagggugaagcuggggugagacccagu
ggaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcua
ggagugaaaagcuaaccgagcccggagauagcugguucuccccgaaauga
cuuuagggucagccucaggcgcugacuggggccuguagagcacugauagg
gcuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccc
agguggagccugggagugagggcgcgagcgauaacguccgcguccgagcg
cgggaacaaccgagaccgccagcuaaggcccccaagucugggcuaagugg
uaaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagc
cauccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccg
aaaaugaucggggcucaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
agggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaa
agagggugagaaucccucucgccguaagcccaaggguuccuacgcaaugg
ucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagc
cgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggggg
gacgcucuaggcuagggggaccggagccauggacgagcccggccagaagc
gcagggugggagguaggcaaauccgccucccaaaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
uccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcgccugcguaggauaggugggagccugugaacccccgccuccgggu
gggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaac
ccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgc
cuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaa
auccgccggagagcgcaaggguagaagggggccugacugcgaggccugca
agccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugg
aagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugau
cucccccgagcguccacagcggcggggagguuuggcaccucgaugucggc
ucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccc
auuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgguc
ucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacga
gaggaccggaagggacgcaccucugguuucccagcugucccuccaggggc
auaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaag
cgggaagcccgccccaagaugaggccucccacggcgucaagccgguaagg
acccgggaagacgacccgguggaugggccggggguguaagcgccgcgagg
cguugagccgaccggucccaaucguccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4j Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
• Resolution: 3.83 Å
• Binding residue (original residue number in PDB): M11 R13 N60 R61 P62 L63 K64 I77 L78 R79 E80 R82 K109 G110 R111 G112 F113 A114 G115 K118 R119 N121 F122 A123 G124 P126 D127 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 K155 M156 A157 G158 H159 Y160 R164 T166 M168 N169 K185 V188 P189 P191 G194 K203
• Binding residue (residue number reindexed from 1): M9 R11 N58 R59 P60 L61 K62 I75 L76 R77 E78 R80 K107 G108 R109 G110 F111 A112 G113 K116 R117 N119 F120 A121 G122 P124 D125 S126 H127 G128 A129 H130 K131 I132 H133 R134 H135 G137 S138 I139 G140 N141 R142 K143 T144 P145 G146 R147 V148 Y149 K150 K152 K153 M154 A155 G156 H157 Y158 R162 T164 M166 N167 K183 V186 P187 P189 G192 K201

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:4v4j, PDBe:4v4j, PDBj:4v4j
• PDBsum: 4v4j
• PubMed: 17940016
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)