Structure of PDB 6yws Chain J Binding Site BS01

Receptor Information
>6yws Chain J (length=243) Species: 367110 (Neurospora crassa OR74A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASILASLSDNRGAYHKRIRKGRGPSSGYGKTAGRGTKGQKAHGHVKPWFQ
GGQTPLIVSHGRKGFVNQFAADMSELNLEKLQEWIEAGRIDPTKPITPKE
IIKSGIIGSSIKDGIKLLGRGKESFKIPVTITVSRASASAIEAIEAAGGK
IVTRFYTKESLKRLVEGKSLHTDKPLPVGKEHVEEILAQARSLKKKYYRL
PDPTSRWDIEYYRDPAHRGYLSHQLAPGESPSLYFKVPTGGEK
Ligand information
>6yws Chain A (length=2820) [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
uauuuuaucggugaguauguagacucggaaugacaaagaugaaucuugaa
uaaucagacauagaaugauaagguuguaugucaaaagggaaacagcccag
aacaagaguuaagguuccaaaauuauuauuaagugaaauaaagaaaguuu
uuauauaagucgacaagaagaugggcuuggaagcagccauaauuuaaaga
ucucguaacagagcacuuguuaaaucuuaaaagcaucgaaaauuuaacgg
aucuaaauaauauaccgaaaccuuguccauauguaacauuaguaauaaua
uuaauguuauuugaugggguagcagaacguugagugaaucuuagauuuuu
uuuuuauaacuaaauauagaugauaacucaagugagaauggugacaugag
uaacaaaaaagaguuuaagguaccuaaaagguaucuuagagucucgccua
aagcuuauggcuacgucaaguaacggccucuaaguuuauaaucugaagau
uaugacgaugagaaaacuuugguaccaacauuuaaaagugaaaauugugc
aggaaggauaaaccguaccuagaaucugaaacaaguaagcuaguagagaa
uacgaaggcgugaaugagauaacaaucauaaaggaacucggcaaacuaac
uaccguaacuuagggauaaggagagcucauuagucucgaacgaguaaaaa
ggaagaagcauggaauauuguuguacgacuguuuaauuaaaacaaagcac
uuugcaaaaagacgauaagucuaaguauugagugugauuucugcccgaug
ccggcugguuaacgaauuuucuaaauugaaaaaaaauuugguuucagagg
aacccccgguuaauggcggccgguccuaagguagcgaaaugccuuggccg
uuaaaugcggucuugcaugaaugauguaacgauacaacagcugucucuau
gauugacucagugaaauuggaauaacugugcagauacaguuuaccucuag
uuagacgagaagacccuaugcagcuuuacuguuacuaauuauugaauacg
auucugaaaauuuccaguguaaaagguaaucgauaagauauaauugaaac
accuuuauuuuucuaucguauuauuaaaccuuaaauuaaggaacaauugu
uagaagacaguuuaugcggggcacaggccccauaaagaguaaaugggugu
gucuaaaauguuugcaauuuuuuauaguauauaucaaaucaucuuuaugc
uauucauagaccuuggguacaguauaaaaauuauauauguauuaauuuac
auauauuuuuucuaagaaauuagguaagauuuuguuuauagagaaauuag
auguaaaaaaaaaaucuuaugagggcggauccgcuucuaauauuuuuuug
uaguuauuauuauaauaauaaucauguuuauuacuuaaaaagcuuaaugg
cuuaaucuugccuuacuguuugauuaacaacaaaucuuacagucgcguaa
gcggggcauaggaucacaagauacaaaaaggaaagaucuuggauuuuugg
aaaagcuacgcuagggauaacaggcuaauuugcgcaagaguguacaaaau
gagugcgcgguuuggcaccucggcuugacuaauccucauggaugcagaaa
cuauguaggguacgacuguucgucgauuaaaaaguuacaugagcuggguu
aaauacgucgugagacaguaugguuucuaucuucuagagggaauuagaau
auaauaaggauuaaccuuuguacgaaaggaacaugggguacuauuguuaa
caguuuuauuaaccucugguuuaccuguuguuuaugugccuuagggaugu
uaccgucacuugaguaaauacaauagcauaagcauggcaggaaagcuaag
uuagucaaaaauaagugcugaaagcauauaggcacgaaauuuaccuuaag
auauuucuuaaauauacguaagaaaauauuacguuaauaggcuuaguuug
uaauaaucuagagauuuuaaggaacuaaguacuaauuuuauaaaaaacug
aaugauuaauauaucuuaca
<<<<..<<<<<<.......<<<<<<<<<..>>>>...<<<.......<<<
<<<<<<<......((.....<<<<<<<<<.<<<<<<.....>>.....<<
<<<<................>>>>>>....>>>>..<<....>>......
....<<<<<<.....<<....>>......>>>>>.>.........<<...
.>>..<<<<<<.....<<....>>....>>>>>>..((............
...<<<<<<<<....>>>>>>>>........<<<<<..<<<<>>>>>...
))......>>>>>>>>>.................<<....>>....))..
.....>>>>>>>>>>.......<<<<..<<.........>>..>>>>...
<............>.<<<<<<....<<<<<<<<<<<<<..<<<.......
..>>>...<......>..<<<<<.....>>>>>...>>>>>>>>>>>>>.
.<<.<..<<<<<<<....<<<<<<<<<<..<<<<<....>>.>>>...<<
<..<<<<........>>>>.>>>....>>>>>>>>>>....<<.....>>
.......>>>>>>.>..>.>>..<<<<<<....<<<<<....>>>>>..<
<<<<<<...<<<<<<.<<.....<<<...<..<<<<<<.<<<<<<<<..<
..<<<<<<<<<..>>>>>>>>>>.>>>>.....>>>>.....<<<<.<<<
..>>>..>>>>>>>>.>>..>..>>.>.....>>.>>>>>>...>>>>>>
>.....<<<<<<.<<<......>>>.>>>>>>....<<<......>>>..
.<<<<<.<<...<<<(((.....<<<<<<.....<<......<<..<<<<
<<<........<<<<<<.<....<<<<.......>>>>....>.......
.<<<......>>>..>>>>>>......>>>>>>>.>>...........))
)>>...>>>>>>.>>>...>>>>>>><<<<..<<<<<<<<<<<<....>>
>>>>>>>>>>...>>>>....>>>>>>..<<<<<<..<<<....<<..<<
..<<...>>..>>..>>....>>>.>>>>>>........>>>>>><....
..<<.....<<<.<<<<<<<<<<<.....>>>>>>>>>>>.>>><<<<<.
..<<<<<.<<........((...<<<.<<<...<<<.<<<<<<<..>>>>
>>>>>>...>>>....)).........<<<.<<..(((((..>>.>>>..
............>>>..>>......<<......>>>>>>>..<<<.....
>>>..>>>>>....<<<<....<<<<<<<<.<<................<
<.<<....<<..>>.....>>>>..<<<.<<..<<<<<..>>>>..>.>>
.>.>>.............<<<<<<<<<..<<<.........>>>..<<<<
<<.......<<<<.....>>>>.......>>>>>>....<<.<<<..<<<
<<<<..<<....<.......<<<<<<<.......>>>>>>>.......>.
...>>>>>>>..>>>>><<<..>>>........<...........<<<<<
<.....>>>>>>.....>....>>.....>>.>>>>>>>.....>>.>>>
>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<
..<<<.[[......<<<<.[[<<<<..<<<<<..<<<<<.<<..<<<<<<
<<...<<<<<...........<<<<<<.<<<.....>>>...........
>>>>>>..>>>>>.>>>>>>>>......<<<<.....>>>>....>>.>>
>>>...>>>>>...<<.......>>.<<<<<<...........>>>>.>>
..<<.....<.......<<<..<<<<...>>>>..>>>.>..........
<<<<<<.......>>>>>>.............<<<<<<<<<......>>>
>>>>>>................<<<<<<<.....<<<<.........>>>
>.<<<<..<<<<<<<.<<<.<<.<<<<<..>>>>>>>>>>.>>>.>>>>.
..<<<<<<<<<..>>>>>>>>>........>>>>......<<<...(((>
>>...>>>>>>>...<<<<..<<<.........>>>..>>>>.<<<....
>>>.>>))).......<<<<<<.(...>>>>...)>>>>>>.........
...>>>>..]]>>>>.......<<<<.<...<<<<<...<.........>
...>>>>>....>>>>.>..<<<<.<<<<<...<<<<<<<<.........
>>>>>..>>>..<<<<.....>>>>.......>>>>..>...>>>.>...
..<<<<<<<....>>>.>>>>....]]..>>>.>>>>>>>.....<<<<<
<...<<<<<...<<<<<...............>.>>......<<<<<..>
>>>>>>.<<<<<<...<<<<...<<<<<<<<<<<<<<.<<<..>>>...<
<<<...)))))..>>>>........>>>>>>>>>..>>>>>...>>>>.>
>>>>>..<<<.<..<<<<<...........>>>>>...>>>>.>>>>>..
.>>>.>>>....<<<.<<<<<.......>>>>>....<<<<<<<<<<<<.
....<<<<....>>>>....>>>.>>>>>>.>>>.....>>>....>>>>
>>>>.....>>>>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6yws Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.
Resolution2.74 Å
Binding residue
(original residue number in PDB)		S48 A51 L53 S54 N56 R57 G58 A59 Y60 H61 K62 R63 I64 R65 K66 G67 R68 G69 P70 S71 S72 Y74 G75 K76 T77 A78 G79 R80 G81 K83 Q85 K86 H88 H90 K92 P93 W94 F95 Q96 G97 Q99 T100 V104 S105 H106 K109 G110 F111 N113 Q114 F115 E121 N123 K126 W130 R135 S155 K162 L164 G165 R166 R181 S183 A184 S185 R209 E212 Y244 R245 P247 D248 T250 S251 R252 W253 Y257 Y280 K282 P284 T285
Binding residue
(residue number reindexed from 1)		S2 A5 L7 S8 N10 R11 G12 A13 Y14 H15 K16 R17 I18 R19 K20 G21 R22 G23 P24 S25 S26 Y28 G29 K30 T31 A32 G33 R34 G35 K37 Q39 K40 H42 H44 K46 P47 W48 F49 Q50 G51 Q53 T54 V58 S59 H60 K63 G64 F65 N67 Q68 F69 E75 N77 K80 W84 R89 S109 K116 L118 G119 R120 R135 S137 A138 S139 R163 E166 Y198 R199 P201 D202 T204 S205 R206 W207 Y211 Y234 K236 P238 T239
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 15:20:36 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 = '6yws', asym_id = 'J', 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='6yws', asym_id='J', 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 = '0003735,0006412,0015934', uniprot = '', pdbid = '6yws', asym_id = 'J'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0006412,0015934', uniprot='', pdbid='6yws', asym_id='J')
    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>