Structure of PDB 5dv5 Chain B Binding Site BS02

Receptor Information

>5dv5 Chain B (length=267) Species: 663 (Vibrio alginolyticus)

KSPAGFAEKYIIESIWNGRFPPGSILPAERELSELIGVTRTTLREVLQRL
ARDGWLTIQHGKPTKVNQFMETSGLHILDTLMTLDVDNATNIVEDLLAAR
TNISPIFMRYAFKANKENSERTIKNVIESCEALMNAASWDDFIASSPYAE
KVLQNVKEDNEKDEAKRQEILIAKTFNFYDYMLFQRLAFHSGNQIYGLIF
NGLKKLYDRVGSYYFSNPASRELALKFYHQLLETCESGQREQLPVVIRHY
GMESALIWNEMKKQLPT

Ligand information

• Ligand ID: PKZ
• InChI: InChI=1S/C37H66N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-28(46)65-21-20-39-27(45)18-19-40-35(49)32(48)37(2,3)23-58-64(55,56)61-63(53,54)57-22-26-31(60-62(50,51)52)30(47)36(59-26)44-25-43-29-33(38)41-24-42-34(29)44/h24-26,30-32,36,47-48H,4-23H2,1-3H3,(H,39,45)(H,40,49)(H,53,54)(H,55,56)(H2,38,41,42)(H2,50,51,52)/t26-,30-,31-,32+,36-/m1/s1
• InChIKey: MNBKLUUYKPBKDU-BBECNAHFSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  OpenEye OEToolkits 1.9.2: CCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.385: CCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  CACTVS 3.385: CCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  ACDLabs 12.01: C(CC(SCCNC(CCNC(C(C(C)(COP(OP(OCC3C(C(C(n2c1ncnc(c1nc2)N)O3)O)OP(O)(O)=O)(=O)O)(O)=O)C)O)=O)=O)=O)CCCCCCCCCCCCC
• Formula: C37 H66 N7 O17 P3 S
• Name: Palmitoyl-CoA
• PDB chain: 5dv5 Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dv5 Snapshort of Vibrio FadR-ligand complex structure reveals a new mechanism for bacterial fatty acid sensing
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): W21 F74 I82
• Binding residue (residue number reindexed from 1): W16 F69 I77
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 15:05:39 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 = '5dv5', asym_id = 'B', bs = 'BS02', title = 'Snapshort of Vibrio FadR-ligand complex structur... a new mechanism for bacterial fatty acid sensing'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5dv5', asym_id='B', bs='BS02', title='Snapshort of Vibrio FadR-ligand complex structur... a new mechanism for bacterial fatty acid sensing')

   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 = '0000062,0003677,0003700,0006355,0019217', uniprot = '', pdbid = '5dv5', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000062,0003677,0003700,0006355,0019217', uniprot='', pdbid='5dv5', 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>