Structure of PDB 6ywy Chain B Binding Site BS01

Receptor Information
>6ywy Chain B (length=315) Species: 5141 (Neurospora crassa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVTPYVRDAGMMRTYKPHTPGIRHLKRPINDHLWKGRPYLPLTFPKKGQS
KGGRNHSGRVTVRHRGGGHKRRIRMVDFERWIPGPHTVLRIEYDPGRSAH
IALVKEEATGRKSYIVAADGMRAGDVVQSYRSGLPQDLLDSMGGVVDPGI
LAARTCWRGNCLPVSMIPVGTQIYCVGSRPDGKAVFCRSAGTYATIISKE
TGKFVNVRLQSGEIRRVSKDACATVGIASNIMHHYRQLGKAGRSRWLNIR
PTVRGLAMNANDHPHGGGRGKSKGNRHPVSPWGTPAKGGYKTRRKSNVNK
WVVTPRVRNMGVRRN
Ligand information
>6ywy Chain A (length=2843) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

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PDB6ywy Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		Y58 R60 K69 P70 H71 T72 P73 G74 R76 H77 R80 W87 K88 G89 R90 Y92 L93 P94 P98 K99 K100 G101 Q102 K104 G105 R107 N108 H109 S110 G111 R112 V113 T114 V115 R116 R118 G119 G120 H122 K123 R124 R125 R127 R143 Y146 P148 R150 S231 R232 V238 F239 C240 R241 S242 A243 G244 T245 L273 Q274 S275 E277 R279 H297 H298 L302 G303 K304 A305 G306 R307 S308 R309 W310 R314 P315 T316 V317 R318 G319 L320 A321 M322 N323 A324 N325 D326 H329 G331 G332 R333 G334 K335 K337 G338 N339 R340 H341 P342 V343 S344 P345 W346 A350 K351 G352 G353 Y354 K355 T356 R357 R358 K359 S360 N363 W365 R370 R372 N373 M374 G375 V376 R377 R378
Binding residue
(residue number reindexed from 1)		Y5 R7 K16 P17 H18 T19 P20 G21 R23 H24 R27 W34 K35 G36 R37 Y39 L40 P41 P45 K46 K47 G48 Q49 K51 G52 R54 N55 H56 S57 G58 R59 V60 T61 V62 R63 R65 G66 G67 H69 K70 R71 R72 R74 R90 Y93 P95 R97 S178 R179 V185 F186 C187 R188 S189 A190 G191 T192 L209 Q210 S211 E213 R215 H233 H234 L238 G239 K240 A241 G242 R243 S244 R245 W246 R250 P251 T252 V253 R254 G255 L256 A257 M258 N259 A260 N261 D262 H265 G267 G268 R269 G270 K271 K273 G274 N275 R276 H277 P278 V279 S280 P281 W282 A286 K287 G288 G289 Y290 K291 T292 R293 R294 K295 S296 N299 W301 R306 R308 N309 M310 G311 V312 R313 R314
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 16 06:06:41 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()
   1435     title=pdb2title(pdbid)
   1436     if bs.startswith("BS"):
=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1438     else:
   1439         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '6ywy', asym_id = 'B', bs = 'BS01', title = 'Analysis of translating mitoribosome reveals fun...eristics of translation in mitochondria of fungi.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6ywy', asym_id='B', bs='BS01', title='Analysis of translating mitoribosome reveals fun...eristics of translation in mitochondria of fungi.')
   1295         display_ec(ec,csaOrig,csaRenu)
   1296     if go:
=> 1297         display_go(go,uniprot,pdbid,asym_id)
   1298     return pubmed,uniprot
   1299 
global display_go = <function display_go>, go = '0003723,0003735,0005840,0006412,0015934,0016740', uniprot = '', pdbid = '6ywy', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003723,0003735,0005840,0006412,0015934,0016740', uniprot='', pdbid='6ywy', asym_id='B')
    480         '''.replace("$namespace_link",namespace_link
    481           ).replace("$namespace",namespace
=>  482           ).replace("$uniprot",u
    483         ))
    484         for l,(term,name) in enumerate(go2aspect[Aspect]):
u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>