Structure of PDB 6ywy Chain R Binding Site BS01

Receptor Information

>6ywy Chain R (length=249) Species: 5141 (Neurospora crassa)

GAYRLKPKRTIPKKLGAKKTGDQYVIPGNIIYKQRGTLWHPGENTIMGRD
HTIHAAVAGYVKYYRDPQLHPDRQYIGVVFNRNDKLPYPKDAPRKRKLGL
VAVPRKVEEVEKPTMSASGLPLFVTRHETISSVIAELIKEKLAARAEYNA
RQSALRKLQQQKMLARRGTRVLRLMNNYSYRETNWEIGRLIGDPGSVPGT
EKVGSRKAKFRARRRRRNTFLLGIKERKLAKADRREEYRRRVREKREQR

Ligand information

>6ywy Chain A (length=2843)

guaauggauauaaagcuuauguuuauauauauauauaaguauauaaagag
acuacuaccaauagcuacacuauguauuaaggagaguauaacuuaauuua
uguuuaugauagagguuaucaacauaugaacucuuagagaaauuacuuaa
uaaacgaagugaauugaaauaucuuauuaacuucaggaaaagaaaucaaa
cgagauucuaugauuagugugaacgaaaauagagcagccuauuaaaauaa
guaaaauggcuuuaaagcuguuugaauauuguggggaaccuuccucaaag
gcuaaauauaauacaugaguuacagagaaaaguaccgugagggaaagcuu
ugaaauaguaguuuuauaagcagcucaagcaauaagaaagcgagagcgua
ccuuuugcauaaugggucaccaaguuaauuuuagaugcgagcgaauuaga
ugugcauaguuaaaccgaucauuaaaauaaugaauagugucuaaaguuag
acccgaagccuggugaucuuacuauagucaggacuauaaagguccgaacg
gguuaucguugcaaagauauccgaagaacuaugguaagcgagugaaagac
aacacugacuaggauagcugguuuucugcgaaaccuauaauaguaggcaa
uuuaaguaacaucuuaguagguacagaacuuaaucucagacaagauguag
auuuucauaccuagguaugaaaugcauuuuuuuuuguauacaucggggga
ucgugaagauuuuaucggugaguauguagacucggaaugacaaagaugaa
ucuugaauaaucagacauagaaugauaagguuguaugucaaaagggaaac
agcccagaacaagaguuaagguuccaaaauuauuauuaagugaaauaaag
aaaguuuuuauauaagucgacaagaagaugggcuuggaagcagccauaau
uuaaagaucucguaacagagcacuuguuaaaucuuaaaagcaucgaaaau
uuaacggaucuaaauaauauaccgaaaccuuguccauauguaacauuagu
aauaauauuaauguuauuugaugggguagcagaacguugagugaaucuua
gauuuuuuuuuuauaacuaaauauagaugauaacucaagugagaauggug
acaugaguaacaaaaaagaguuuaagguaccuaaaagguaucuuagaguc
ucgccuaaagcuuauggcuacgucaaguaacggccucuaaguuuauaauc
ugaagauuaugacgaugagaaaacuuugguaccaacauuuaaaagugaaa
auugugcaggaaggauaaaccguaccuagaaucugaaacaaguaagcuag
uagagaauacgaaggcgugaaugagauaacaaucauaaaggaacucggca
aacuaacuaccguaacuuagggauaaggagagcucauuagucucgaacga
guaaaaaggaagaagcauggaauauuguuguacgacuguuuaauuaaaac
aaagcacuuugcaaaaagacgauaagucuaaguauugagugugauuucug
cccgaugccggcugguuaacgaauuuucuaaauugaaaaaaaauuugguu
ucagaggaacccccgguuaauggcggccuuagcgugaggguccuaaggua
gcgaaaugccuuggccguuaaaugcggucuugcaugaaugauguaacgau
acaacagcugucucuaugauugacucagugaaauuggaauaacugugcag
auacaguuuaccucuaguuagacgagaagacccuaugcagcuuuacuguu
acuaauuauugaauacgauucugaaaauuuccaguguaaaagguaaucga
uaagauauaauugaaacaccuuuauuuuucuaucguauuauuaaaccuua
aauuaaggaacaauuguuagaagacaguuuaugcggggcacaggccccau
aaagaguaaaugggugugucuaaaauguuugcaauuuuuuauaguauaua
ucaaaucaucuuuaugcuauucauagaccuuggguacaguauaaaaauua
uauauguauuaauuuacauauauuuuuucuaagaaauuagguaagauuuu
guuuauagagaaauuagauguaaaaaaaaaaucuuaugagggcggauccg
cuucuaauauuuuuuuguaguuauuauuauaauaauaaucauguuuauua
cuuaaaaagcuuaauggcuuaaucuugccuuacuguuugauuaacaacaa
aucuuacagucgcguaagcggggcauaggaucacaagauacaaaaaggaa
agaucuuggauuuuuggaaaagcuacgcuagggauaacaggcuaauuugc
gcaagaguguacaaaaugagugcgcgguuuggcaccucgaugucggcuug
acuaauccucauggaugcagaaacuauguaggguacgacuguucgucgau
uaaaaaguuacaugagcuggguuaaauacgucgugagacaguaugguuuc
uaucuucuagagggaauuagaauauaauaaggauuaaccuuuguacgaaa
ggaacaugggguacuauuguuaacaguuuuauuaaccucugguuuaccug
uuguuuaugugccuuagggauguuaccgucacuugaguaaauacaauagc
auaagcauggcaggaaagcuaaguuagucaaaaauaagugcugaaagcau
auaggcacgaaauuuaccuuaagauauuucuuaaauauacguaagaaaau
auuacguuaauaggcuuaguuuguaauaaucuagagauuuuaaggaacua
aguacuaauuuuauaaaaaacugaaugauuaauauaucuuaca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ywy Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
• Resolution: 3.05 Å
• Binding residue (original residue number in PDB): G67 A68 R70 L71 K72 P73 K74 R75 T76 I77 K79 K80 K84 T86 G87 Q89 P93 N95 I96 Y98 K99 R101 G102 T103 W105 R115 D116 H117 H120 Y129 H136 R148 P159 K161 K172 R192 I255 K258 L259 R262 Y265 L289 M292 N294 Y297 R298 N301 W302 R306 P311 G312 V314 S322 R323 K324 F327 R328 R330 R331 R334 K342 R344 K345 L346 R351 R352 Y355 R356 R358 R363
• Binding residue (residue number reindexed from 1): G1 A2 R4 L5 K6 P7 K8 R9 T10 I11 K13 K14 K18 T20 G21 Q23 P27 N29 I30 Y32 K33 R35 G36 T37 W39 R49 D50 H51 H54 Y63 H70 R82 P93 K95 K106 R126 I138 K141 L142 R145 Y148 L172 M175 N177 Y180 R181 N184 W185 R189 P194 G195 V197 S205 R206 K207 F210 R211 R213 R214 R217 K225 R227 K228 L229 R234 R235 Y238 R239 R241 R246

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ywy, PDBe:6ywy, PDBj:6ywy
• PDBsum: 6ywy
• PubMed: 33056988
• UniProt: Q8X0Q2