Structure of PDB 5umd Chain W Binding Site BS01

Receptor Information

>5umd Chain W (length=170) Species: 36329 (Plasmodium falciparum 3D7)

YAKKIRNLGKCAKGAGVDLRVHFKNTYEAARAIRRMKLLEAKKYLNDVIE
KKRCVPFRKYNGGVGRTNQAKEFNHTQGRWPAKSCKFLLNILDNVQANAE
SRNLDVSKLRLIHVMVNKARPGRRRTYKAHGRINPFMSSPCHIQIIAREI
NISNQNRLKNKSVKKQQTVQ

Ligand information

>5umd Chain A (length=3191)

gauguuaggagggcaaauccgccgaauuuaagcauauaauuaagcggaag
aaaagaaaauaacuaugauuccuuuaguaacggcgagugaacaaggacca
gcucaaacgguuaauccuucguuuggugcaaaccuuucgacggaauuguc
guugaauuauuccaugaaugccuuuaauuugagcaaagugagcaggaaug
cuuccccauagagggugaaaggcccauaguucuuuuuaauuuauucauug
gaauuuuucaugucgagucguguucuuugagauuggagcacuaauacgug
ugauacauuucacauaaagcuaaauauauguaggagaccgauagcaaaca
aguaccgugagggaaagaugaaauaguacucaggaaugagcaauuaaaua
guaccugaaaucguuaagauggaacggauuaagagagaaaacaaguaaag
aggggaauauucucuucuuuauuaaaagaaacaucagugauuaauuuaau
uucaauaaagcaauccccugaaauuguuuucacuuucuccccgcacuaau
guggggaaaacuggcuuuauuucuucaauuauuuuuuuugcugaggaauu
uuaaaauuauuugaauuuuucuucuuauaauuuaaguuguuucuauacag
uacuuucuuaacccacucgucuugaaacacggaccaaggagucuagcaaa
ugugcaaguguauaugauucuuuaaacauuuuacgcauaauuaauguaau
auguccauuguagauuugugccccacuuugcauacaauaccgguaagcaa
augcuuuauugaguacgagcauauuugguaggacccgagaggcuuugaac
uaagcgugaugagauugaagucagacgaaagucugauggaggaucgaguu
gauacugacgugcaaaucguucauuucaaucacguuuaggggcgaaagac
uaaucgaaaagccuauuagcugguuauuuucgaaagaucucucaggaucg
cuggaguugauuaauauaauuuuaccagguagagauaaugauuagaggac
agggccuugaccuauucucaaacucccaauagguaaaaagggcgaaauaa
cucaauuuguauuucacucauauuaaauaaaauaacuccaagugggccau
uuuugguaagcagaacuggcgaugagggaugcuccuaacgcuuggauaag
gugccuaaauauucgcucaugagaucccauaaaagguguugguucauaug
aacuagcccugaaaauggauggcgcuaaagcggauuaccgauaccaagcc
auaaaaagaagaaaaaauuuuuuuuuagaaucuuuuuaugaguagaaaau
cgugggguuuguguugaagcgaaauacgugaguuuucguggaacaucucc
cuagugcagaucuugguggaaguagcaacuauucaaaugagaacuuugaa
gacugaaguggagaaggguuucuugucaacugugauugaacaagaguuag
ccgcuccuaagggauagcugaaaaguguuuaaagggguccccgucucaaa
agggaaacagguugauauuccugugccaauaguauuaugaguuagauggu
aacauauauauaaaugaacuccuuuacauaggcuuuacacucggggugcg
uuuucuuugcacuuuaccuuuauaacaaaccuuggaaucaauuuacuugg
agaagagguucguugaacucaauucaaaaauuuguuuuguagcaauagua
auucguaauuauccgaagugguaaggacuauccuugaaaaaaggagggaa
cggcuuugugcuuugcuacucuuaauacuuguaugagcguaccaacaacc
gcaucaggucuccaagguuaacagccucugguuaaauagaaaaaaguagg
uaagggaagucggcaaaauagauccguaacuucgggaaaaggauuggcuc
ugaggacauuaauguuaacucagaacugaaacggacaaggggaauccgac
uguuuaauuaaaacauagcauugugaaaagccacaacugguauuaacaca
augugauuucugcccagugcuuugaaugucaacuugaugaaauucaauca
agcgcagguaaacggcgggaguaacuaugacucucuuaagguagccaaau
gccucgucaucuaauuagugacgcgcaugaauggauuaacgagauuccca
cugucccuacuugcuaucuagcgaaaccacagccaagggaacgggcuugg
caaaaucagcggggaaagaagacccuguugagcuuuacucuagucuggcu
uugugaaacgacuuaagaggugcuacuuuuaaaguuguuuuacuuaucca
uuuauagggaugaauuucccaauauggagacauagccagguggggaguuu
gacuggggcgguacaucuguuaaauauuaacgcagauguccaaagacaag
cucaaagagaacagaaaucucuuguagacuaaaaggggaaaagcuuguuu
gauuucuauuuucagaacaaguagaaaacgugaaagcguggccuaucgau
ccuuuauauuugcaaaaugacguaaauuacuuacuacugugcauauagag
gugucugaaaaguuaccacagggauaacuggcuuguggcugccaagcgcu
ccuagcgacguagcuuuuugauccuucgaugucggcucuuccuaucauug
ggacgcagaagucucaaagugucggauuguucacccgcuaauagggaacg
ugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugaug
aauuuuauuauauauauacauauaguauugugacaguaauccaacuuggu
acgagaggauuaguugguucagacaauugguacagcaauugguugacaaa
ccaguguugcgaagcuaagucuguuggauaauggcugaacgccucuuaag
ccagaaaccaugcugauuaaacaauacuaucuuuuuuguuugcuaaugua
aaagagaaauuauauauguaccgguacauaaauaauccuaucaccuuuuu
cguggcuagcugugagcuaggcaauaguucuuuaacaacaaaaaagagca
caaacuguagacgacuuuuuugccucagggugcuguaaacaugaaaguaa
acuuuacgaucuguugaggcuuaucccuagugguaaagugu

.................<<<<<......<......>.......>>>>>..
..<.....<<....>>...<<<<<.....<<.....>>....>>>>>...
<<<...<<<.....<<<.<<<...<<<....>>>...>>>.>>>.....>
>>.<<<..<<<<<<<<<<<....<<<<...<<<<.....<<<<......>
>>>.((......<<<.....))>>>...>>>>...>>>>...>>>>>.>>
>>>>..>>>..........<<<<<<<........>>>>>>>......<<<
<<..[[((((>>>>>..>>>....>.........................
....<<....>>................<<<<....>>>>..........
.........................<<.<<<<<<<<<.......<<<<<<
<<<<<<<..>>>>>>>>>>>>>....<<<<<<<.<<<<<<..<<..<<<<
...<<<<<<<<.......<<<<......>>>>.<<..<<<<<<.......
.>>>>>>>>....>>>>>>>>......>>>>..>>..>>>>>>.......
....<<<<<<..<<<......>>>..>>>>>>.....>>>>>>>......
..>>>>>>>>>.>>..<<<<........>>>><<<<<<...<<<<.<<<<
<<<<<..<<<...<<<..........>>>....>>>...<<....>>...
.......<<<<<.<...<<.....>>..>...>>>>><<<<<<<<<<<..
..>>>.>>>>>.>>>...>>>>>>>>>.>>>>.<<.<..<<<<<<<....
.<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>....<
<..<<.<<........>>>>.>>.....>>>>>>>>>...<<.......>
>......>>>>>>...>..>.>>..<<<<<<....<<<<<....>>>>><
<<<<<<<<........<<.<<<<<<<.....<<<....<<<....<<<.<
<<<..>>>>.>>>....>>>..>>.>.....>>>>>...<<<.<<<<<<.
<.......>>>>>>>.>>>......>>>>....>>>>>>>.>>..<<<<.
<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<....<
<<(((.....<<<<<<.....<<..........<<<.<<<<<<<<<..>>
>>>>>>>>>>..........))).>>...>>>>>>.>>>....>>>>>><
<<<<<<<<...<<<<<<..>>>>>>......>>>>>>>>>....>>>>>>
..<<<<<..<<<......<<<<<<.<<....>>>>>>>>...>>>...>>
>>>........>>>>>><<.....<<.....<<<<<<.......>>>>>>
<<<<.....<<<<<.<<...<<<<<<...<.......>.>>>>>>....(
(<<<<<<...<<<<..<<<....>>>.......<<<<.>>>>.>>>>...
.>>...<<<<<........>>>>>))<...<<<<<<<.<<<<...<<<..
..>>>...........((<<<<<<...<<<<.<<<<<<<<<..<<<<<<<
...{{..>>>>>>....<<...<<<<.<<<<<<.....<<<.....>>>.
....>>>>>>.>>>>....<<<..<<<<..>>>>..>>>.>>.....<..
<.<....>.>..>>..>>>.>>>>>>.>>>>.........>>>>>>....
.<<<...<..>...>>>>>>>.>>>>>>>.....>>>>>..>>.....<<
......>>>>>>>.<<<<.....>>>>..>>>>...<<<<....<<<<<<
<<.<<.........<.....<<<<<....<....>.....>>>>><<.<<
<<<<<<<<<..>>>>>..>>>>>>.>>............<<<<<<<<<..
<<<.........>>>..<<<<<<<.....<<<<....>>>>......>>>
>>>>.<.<<..<<<..<<<<<<.<..<<<....<<<<......>>>>...
.>>>>>>>>..>>>>><<<<<<.......>>>>>>........<......
.....<<<<<.......>>>>>.....>.....>>.>..>>.>>>>>>>.
.>..>>.>>>>>>>>.>>>>>>....>>....<<<<<........>>>>>
....<<<<<..<<<.<<......<<<<.<<<<<<..<<<<<.<<<<<<<<
..<<<<<<<<<<<<<<<<<......>>>>>>.>>>>>>>>>>>...<<<<
<.....<<<<....))>>>>...>>>>>.....>>>>>>>>..>>>>>..
.<<<.....>>>..<<<<<<...........>>>>>>..<<...<<<<<<
<...<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>.
..<<<<<<<<<.......>>>>>>>>>.<<<....>>>.>>)))......
<<<<<<<...<<<.))))...<<<<.....>>>>....]]>>>.>>>>>>
>.........>>>>..>>>>>>.......<<.<...<<<<<<...<<...
....>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<<<<<
<<<<......>>>>>>>..>>.<<<.........>>>.....>>>>>..>
...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>.
.....<<<.<<<..>>>..>>><<<<<<<<<..<<<<.<.<<<<<<....
...........>>>>>>.><<<<<...<<<<...<<<<<<<<<<}}..>>
>>>..>>>>>...>>>>.>>>>>.<<<....<<<<<............>>
>>>....>>>.>>>>.....>>>>>>>>>.<<<<<<<<<.......<<<.
.....<<.......<<<<<<<<>>>>>>>>.....>>......<<<..<<
<<<<<<..>>>>>>>>..>>>.............>>>>>>>>>>>>.<<<
<.<<.............>>..<<<..<<<<.<<<....<<<.<<..<<<<
<.>>>>>..>>>>>...>>>....>>>>...>>>...>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5umd Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): Y4 K6 K16 A18 R23 H25 F26 K27 Y30 R34 R37 R38 R56 K62 Y63 N64 G65 G66 G68 R69 N71 K74 E75 N77 T79 Q80 R82 W83 P84 A85 K86 N97 A100 N101 S104 R105 R113 M118 V119 K121 R123 R127 T129 Y130 K131 A132 H133 G134 I136 N137 P138 F139 M140 S141 S142 R151 I153 Q188 N189 S195 V196 K198
• Binding residue (residue number reindexed from 1): Y1 K3 K13 A15 R20 H22 F23 K24 Y27 R31 R34 R35 R53 K59 Y60 N61 G62 G63 G65 R66 N68 K71 E72 N74 T76 Q77 R79 W80 P81 A82 K83 N94 A97 N98 S101 R102 R110 M115 V116 K118 R120 R124 T126 Y127 K128 A129 H130 G131 I133 N134 P135 F136 M137 S138 S139 R148 I150 Q155 N156 S162 V163 K165

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5umd, PDBe:5umd, PDBj:5umd
• PDBsum: 5umd
• PubMed: 28288098
• UniProt: Q8IDI5