Structure of PDB 7m4x Chain W Binding Site BS01

Receptor Information

>7m4x Chain W (length=77) Species: 480119 (Acinetobacter baumannii AB0057)

SKVCQVTGKRPVVGNNVSHANNKTKRRFEPNLHHHRFWLESEKRFVRLRL
TTKGMRIIDKLGIEKVVADLRAQGQKI

Ligand information

>7m4x Chain A (length=2730)

gucaaguaauuaagugcaugugguggaugccuuggcagucagaggcgaug
aaagacgugauagccugcgaaaagcuccggggaggcggcaaauauccuuu
gauccggagaugucugaaugggggaacccaccuacuuuaagguagguauu
gcaacaugaauacauaguguugcaaggcgaacgaggggaagugaaacauc
ucaguacccuuaggaaaagaaaucaauugagauucccucaguagcggcga
gcgaacggggaucagcccauuaaguuauguguguuuuaguggaacgcucu
gggaagugcgaacguagagggugauauucccguacacgaaagggcacaca
uaaugaugacgaguagggcgaggcacgugaaaccuugucugaauaugggg
ggaccauccuccaaggcuaaauacuccugacugaccgauagugaaccagu
accgugagggaaaggcgaaaagaaccccugugaggggagugaaauagauc
cugaaaccgcaugcauacaagcagugggagcaccuucguggugugacugc
guaccuuuuguauaaugggucagcgacuuauauucaguagcgagguuaac
cguauaggggagccguagagaaaucgagucuuaauagggcguuuaguugc
uggguauagacccgaaaccaggcgaucuauccaugagcagguugaagguu
ggguaacacuaacuggaggaccgaacccacugucguugaaaagccagggg
augacuuguggauaggggugaaaggcuaaucaagccuggugauagcuggu
ucuccccgaaagcuauuuagguagcgccucggacgaauaccauagggggu
agagcacuguuucggcaccgaugcaaacuccgaauaccuaugaguacuau
ccgggagacagacugcgggugcuaacguccguagucaagaggaaaacaau
ccagaccgccagcuaaggccccaaaaucauaguuaagugggaaacgaugu
gggaaggcauagacagcuauagucgagucggccugcgcggaagauguaac
ggggcuaaaacuaugugccgaagcugcggauguauacuuuguauacgugg
uaggggagcguucuguaagccgaugaagguguguugagaagcaugcugga
gguaucagaagugcgaaugcugacgugaguaacgacaaaacgggugaaaa
acccguucgccgaaagaccaaggguuccaguccaacguuaaucggggcug
ggugagucgaccccuaaggcgaggccgaaaggcguagucgaugggaaaau
gguuaauauuccauuacuucuguguaaugcgaugagaggacggagaaggc
uaaaucagccuggcguugguuguccaggugaaaggauguaggcauguauc
uuaggcaaauccgggguacucuaugcugagaucugauagcaagcuguacu
ugugcagcgaagugguugaugccaugcuuccaggaaaagucucuaagcuu
caguuacacaggaaucguacccgaaaccgacacagguggucaggucgagu
agaccaaggcgcuugagagaacucugcugaaggaacuaggcaaaauggua
ccguaacuucgggagaagguacgcuguuguuggugauggaacucgcuucc
ugagcugacgacagccgcagaaaccaggccgcugcaacuguuuauuaaaa
acauagcacucugcaaacacgaaaguggacguauagggugugaugccugc
ccggugcuggaagguuaauugaugggguuagcguaagcgaagcucuugau
cgaagccccaguaaacggcggccguaacuauaacgguccuaagguagcga
aauuccuugucggguaaguuccgaccugcacgaauggcauaaugauggcg
gcgcugucuccagcagaggcucagugaaaucgaaaucgcugugaagaugc
aguguacccgcggcuagacggaaagaccccgugaaccuuuacugcagcuu
gacacugaacuuugauugagguucuaacucugucccgugauccgggacga
ggaccgugucugguggguaguuugacuggggcggucuccuccuaaagagu
aacggaggaguacgaaggugcgcucagcguggucggaaaucacgcguaga
guauaaaggcaaaagcgcgcuuaacugcgagacccacaagucgagcaggu
acgaaaguaggucuuagugauccggugguucuguauggaagggccaucgc
ucaacggauaaaagguacucuggggauaacaggcugauaccgcccaagag
uucauaucgacggcgguguuuggcaccucgaugucggcucaucucauccu
ggggcugaagcaggucccaaggguauggcuguucgccauuuaaagaggua
cgcgagcuggguuuagaacgucgugagacaguucggucccuaucuaccgu
gggcgcuggaaauuugagaggaucugcuccuaguacgagaggaccagagu
ggacgaaccucugguguaccgguugugacgccagucgcaucgccggguag
cuauguucggaagggauaaccgcugaaagcaucuaagcgggaagccuacc
ucaagauaagauuucccuaggacuuuauguccucuaaagagccguucgag
acuaggacguugauagguuggauguggaagcauagugauaugugaagcug
accaauacuaauugcucgugaggcuugacu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m4x Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii.
• Resolution: 2.66 Å
• Binding residue (original residue number in PDB): S2 K3 K10 V13 N16 S19 H20 A21 N22 N23 K26 R27 F29 E30 P31 N32 H34 H36 R37 R50 T53 R57 K61 L62
• Binding residue (residue number reindexed from 1): S1 K2 K9 V12 N15 S18 H19 A20 N21 N22 K25 R26 F28 E29 P30 N31 H33 H35 R36 R49 T52 R56 K60 L61

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 11:56:50 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 = '7m4x', asym_id = 'W', bs = 'BS01', title = 'Cryo-EM Determination of Eravacycline-Bound Stru...rug Efflux Pump AdeJ of Acinetobacter baumannii. '

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7m4x', asym_id='W', bs='BS01', title='Cryo-EM Determination of Eravacycline-Bound Stru...rug Efflux Pump AdeJ of Acinetobacter baumannii. ')

   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', uniprot = '', pdbid = '7m4x', asym_id = 'W'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003735,0005840,0006412', uniprot='', pdbid='7m4x', asym_id='W')

    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>