Structure of PDB 5umd Chain a Binding Site BS01

Receptor Information

>5umd Chain a (length=106) Species: 36329 (Plasmodium falciparum 3D7)

AQRVHYRRHNHYNTKSNKVRPVRTPGGKLTIHVVKKKAGKPKCADCKTAI
QGVKALRPADNYRARRKNRTVARAYGGSICARCIRERIMRAFLFEEQKCV
RQVLKE

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): A2 R4 V5 H6 Y7 R8 R9 H10 N11 H12 Y13 N14 T15 K16 S17 K19 R21 P22 V23 R24 T25 P26 G27 L30 T31 H33 K36 K37 K38 A39 G40 K41 K43 A45 Q52 G53 V54 K55 A56 R58 P59 A60 N62 Y63 R64 R66 R67 K68 N69 R70 T71 V72 A73 R74 A75 Y76 G78 A82 R83 R91 A92 E96 K99
• Binding residue (residue number reindexed from 1): A1 R3 V4 H5 Y6 R7 R8 H9 N10 H11 Y12 N13 T14 K15 S16 K18 R20 P21 V22 R23 T24 P25 G26 L29 T30 H32 K35 K36 K37 A38 G39 K40 K42 A44 Q51 G52 V53 K54 A55 R57 P58 A59 N61 Y62 R63 R65 R66 K67 N68 R69 T70 V71 A72 R73 A74 Y75 G77 A81 R82 R90 A91 E95 K98

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

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

External links

• PDB: RCSB:5umd, PDBe:5umd, PDBj:5umd
• PDBsum: 5umd
• PubMed: 28288098
• UniProt: Q8IBY4