Structure of PDB 8g60 Chain SX Binding Site BS01

Receptor Information

>8g60 Chain SX (length=142) Species: 9606 (Homo sapiens)

GKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIV
LEKVGVEAKQcNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVL
VAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGKKERPRS

Ligand information

>8g60 Chain S2 (length=1654)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucccacuuggauaacugugguaa
uucuagagcuaauacaugccgacgggcgcugacccgggggaugcgugcau
uuaucaguggugacucuagauaaccucgggccgaucgcacgccccccgug
gcggcgacgacccauucgaacgucugcccuaucaacuuucgaugguaguc
gccgugccuaccauggugaccacgggugacggggaaucaggguucgauuc
cggagagggagccugagaaacggcuaccacauccaaggaaggcagcaggc
gcgcaaauuacccacucccgacccggggagguagugacgaaaaauaacaa
uacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaaucc
uuuaacgaggauccauuggagggcaagucuggugccagcagccgcgguaa
uuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcucgua
guuggaucuuguuacuuugaaaaaauuagaguguucaaagcaggcccgag
ccgccuggauaccgcagcuaggaauaauggaauaggaccgcgguucuauu
uuguugguuuucggaacugaggccaugauuaagagggacggccgggggca
uucguauugcgccgcuagaggugaaauucuuggaccggcgcaagacggac
cagagcgaaagcauuugccaagaauguuuucauuaaucaagaacgaaagu
cggagguucgaagacgaucagauaccgucguaguuccgaccauaaacgau
gccgaccggcgaugcggcggcguuauucccaugacccgccgggcagcuuc
cgggaaaccaaagucuuuggguuccggggggaguaugguugcaaagcuga
aacuuaaaggaauugacggaagggcaccaccaggaguggagccugcggcu
uaauuugacucaacacgggaaaccucacccggcccggacacggacaggau
ugacagauugauagcucuuucucgauuccgugggugguggugcauggccg
uucuuaguugguggagcgauuugucugguuaauuccgauaacgaacgaga
cucuggcaugcuaacuaguuacgcgacccccgagcggucggcguccccca
acuucuuagagggacaaguggcguucagccacccgagauugagcaauaac
aggucugugaugcccuuagauguccggggcugcacgcgcgcuacacugac
uggcucagcgugugccuacccuacgccggcaggcgcggguaacccguuga
accccauucgugauggggaucggggauugcaauuauuccccaugaacgag
gaauucccaguaagugcgggucauaagcuugcguugauuaagucccugcc
cuuuguacacaccgcccgucgcuacuaccgauuggaugguuuagugaggc
ccucggaucggcccgagcgcugagaagacggucgaacuugacuaucuaga
ggaaguaaaagucguaacaagguuuccguaggugaaccugcggaaggauc
auua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g60 mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.54 Å
• Binding residue (original residue number in PDB): G2 K3 C4 R5 G6 R8 T9 R11 K12 H16 R17 R18 Q20 K21 W22 H23 D24 K25 K28 A44 S45 H46 A47 K48 N63 S64 A65 I66 R67 K68 K76 P86 N87 D88 G89 G104 G106 R107 K108 H110 V112 G113 D114 R119 K121 K124 S129 K137
• Binding residue (residue number reindexed from 1): G1 K2 C3 R4 G5 R7 T8 R10 K11 H15 R16 R17 Q19 K20 W21 H22 D23 K24 K27 A43 S44 H45 A46 K47 N62 S63 A64 I65 R66 K67 K75 P85 N86 D87 G88 G103 G105 R106 K107 H109 V111 G112 D113 R118 K120 K123 S128 K136

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 23:24:01 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 = '8g60', asym_id = 'SX', bs = 'BS01', title = 'mRNA decoding in human is kinetically and structurally distinct from bacteria.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8g60', asym_id='SX', bs='BS01', title='mRNA decoding in human is kinetically and structurally distinct from bacteria.')

   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 = '0003735,0005840,0006412,0015935', uniprot = '', pdbid = '8g60', asym_id = 'SX'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412,0015935', uniprot='', pdbid='8g60', asym_id='SX')

    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>