Structure of PDB 5v7q Chain D Binding Site BS01

Receptor Information

>5v7q Chain D (length=213) Species: 1773 (Mycobacterium tuberculosis)

ARKGILGTKLGMTQVFDESNRVVPVTVVKAGPNVVTRIRTPERDGYSAVQ
LAYGEISPRKVNKPLTGQYTAAGVNPRRYLAELRLDDSDAATEYQVGQEL
TAEIFADGSYVDVTGTSKGKGFAGTMKRHGFRGQGASHGAQAVHRRPGSI
GGCATPARVFKGTRMAGRMGNDRVTVLNLLVHKVDAENGVLLIKGAVPGR
TGGLVMVRSAIKR

Ligand information

>5v7q Chain A (length=3118)

aagugucuaagggcgcaugguggaugccuuggcaucgagagccgaugaag
gacgugggaggcugcgauaugccucggggagcugucaaccgagcguggau
ccgaggauuuccgaauggggaaacccagcacgagugaugucgugcuaccc
gcaucugaauauauagggugcgggagggaacgcggggaagugaaacaucu
caguacccguaggaggagaaaacaauugugauuccgcaaguaguggcgag
cgaacgcggaacaggcuaaaccgcacgcauggguaaccggguagggguug
ugugugcgggguugugggaggauaugucucagcgcuacccggcugagagg
cagucagaaagugucgugguuagcggaaguggccugggauggucugccgu
agacggugagagcccgguacgcgaaaacccggcaccugccuaguaucaau
ucccgaguagcagcgggcccguggaauccgcugugaauccgccgggacca
cccgguaagccuaaauacuccucgaugaccgauagcggauuaguaccgug
agggaauggugaaaaguaccccgggaggggagugaaagaguaccugaaac
cgugugccuacaauccgucagagccuccuuuuccucuccggaggagggug
gugauggcgugccuuuugaagaaugagccugcgagucagggacaugucgc
aagguuaacccgugugggguagccgcagcgaaagcgagucugaauagggc
gacccacacgcgcauacgcgcgugugaauaguggcguguucuggacccga
agcggagugaucuacccauggccagggugaagcgcggguaagaccgcgug
gaggcccgaacccacuuagguugaagacugaggggaugagcuguggguag
gggugaaaggccaaucaaacuccgugauagcugguucuccccgaaaugca
uuuaggugcagcguugcgugguucaccgcggagguagagcuacuggaugg
ccgauggguuacugacgucagccaaacuccgaaugccgugguguaaagcg
uggcagugagacggcgggggauaagcuccguacgucgaaagggaaacagc
ccagaucgccggcuaaggcccccaagcgugugcuaagugggaaaggaugu
gcagucgcaaagacaaccaggagguuggcuuagaagcagccacccuugaa
agagugcguaauagcucacuggucaagugauugugcgccgauaauguagc
ggggcucaagcacaccgccgaagccgcggcacauccaccuuguggugggu
guggguaggggagcgucccucauucagcgaagccaccgggugaccggugg
uggagggugggggagugagaaugcaggcaugaguagcgacaaggcaagug
agaaccuugcccgccgaaagaccaaggguuccugggccaggccaguccgc
ccagggugagucgggaccuaaggcgaggccgacaggcguagucgauggac
aacggguugauauucccguacccgugugugggcgcccgugacgaaucagc
gguacuaaccacccaaaaccggaucgaucacuccccuucgggggugugga
guucuggggcugcgugggaacuucgcugguaguagucaagcgaaggggug
acgcaggaagguagccguaccagucagugguaacacuggggcaagccggu
agggagagcgauaggcaaauccgucgcucacuaauccugagaggugacgc
auagccgguugaggcgaauucggugauccucugcugccaagaaaagccuc
uagcgagcacacacacggcccguaccccaaaccgacacagguggucaggu
agagcauaccaaggcguacgagauaacuaugguuaaggaacucggcaaaa
ugcccccguaacuucgggagaagggggaccggaauaucgugaacacccuu
gcggugggagcgggauccggucgcagaaaccagugaggagcgacuguuua
cuaaaaacacagguccgugcgaagucgcaagacgauguauacggacugac
gccugcccggugcuggaagguuaagaggacccguuaacccgcaaggguga
agcggagaauuuaagccccaguaaacggcggugguaacuauaaccauccu
aagguagcgaaauuccuugucggguaaguuccgaccugcacgaauggcgu
aacgacuucucaacugucucaaccauagacucggcgaaauugcacuacga
guaaagaugcucguuacgcgcggcaggacgaaaagaccccgggaccuuca
cuacaacuugguauugauguucgguacgguuuguguaggauaggugggag
acugugaaaccucgacgccaguuggggcggagucguuguugaaauaccac
ucugaucguauugggcaucuaaccucgaacccugaaucggguuuagggac
agugccuggcggguaguuuaacuggggcgguugccuccuaaaauguaacg
gaggcgcccaaagguucccucaaccuggacggcaaucagguggcgagugu
aaaugcacaagggagcuugacugcgagacuuacaagucaagcagggacga
aagucgggauuagugauccggcacccccgaguggaaggggugucgcucaa
cggauaaaagguaccccggggauaacaggcugaucuuccccaagagucca
uaucgacgggaugguuuggcaccucgaugucggcucgucgcauccugggg
cuggagcaggucccaaggguugggcuguucgcccauuaaagcggcacgcg
agcuggguuuagaacgucgugagacaguucggucucuauccgccgcgcgc
gucagaaacuugaggaaaccugucccuaguacgagaggaccgggacggac
gaaccucuggugcaccaguugucccgccaggggcaccgcuggauagccac
guucggucaggauaaccgcugaaagcaucuaagcgggaaaccuucuccaa
gaucagguuucucacccacuuggugggauaaggccccccgcagaacacgg
guucaauaggucagaccuggaagcucaguaauggguguagggaacuggug
cuaaccggccgaaaacuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v7q Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): M13 T14 R40 Y47 R60 K61 N63 K64 P65 Q69 R79 E83 R85 K119 G120 K121 F123 G125 M127 K128 R129 F132 R133 G134 Q135 G136 H139 G140 Q142 V144 H145 R146 R147 G149 S150 I151 G152 G153 C154 A155 T156 P157 A158 R159 V160 F161 R165 M166 A167 R169 N172 R174 T176 L178 A197 V198 P199 I212
• Binding residue (residue number reindexed from 1): M12 T13 R39 Y46 R59 K60 N62 K63 P64 Q68 R78 E82 R84 K118 G119 K120 F122 G124 M126 K127 R128 F131 R132 G133 Q134 G135 H138 G139 Q141 V143 H144 R145 R146 G148 S149 I150 G151 G152 C153 A154 T155 P156 A157 R158 V159 F160 R164 M165 A166 R168 N171 R173 T175 L177 A196 V197 P198 I211

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5v7q, PDBe:5v7q, PDBj:5v7q
• PDBsum: 5v7q
• PubMed: 28977617
• UniProt: P9WH87|RL3_MYCTU Large ribosomal subunit protein uL3 (Gene Name=rplC)