Structure of PDB 8bgw Chain B Binding Site BS03

Receptor Information

>8bgw Chain B (length=750) Species: 85698 (Achromobacter xylosoxidans)

MGPYRRLWFTLIAVLAVTFALLGFYGGEVYRQAPPIPEEVASADGTRLFG
RDDILDGQTAWQSIGGMQLGSIWGHGAYQAPDWTADWLHRELMAWLDLAA
RDAHGRDYGQLDAPAQAALREQLKAEYRANRADAAGGKLTLSPRRAQAVA
QTEAYYDQLFSDAPALHRSRENYAMKENTLPDANRRRQMTHFFFWTAWAA
ATEREGTSVTYTNNWPHEPLIGNHPSSENVMWSIISVVVLLAGIGLLIWA
WAFLRGKEEDEPPAPARDPLTTFALTPSQRALGKYLFLVVALFGFQVLLG
GFTAHYTVEGQKFYGIDLSQWFPYSLVRTWHIQSALFWIATGFLAAGLFL
APLINGGRDPKYQKAGVDILFWALVLVVVGSFAGNYLAIAQIMPPDLNFW
LGHQGYEYVDLGRLWQIGKFAGICFWLVLMLRGIVPALRTPGGDKNLLAL
LTASVGAIGLFYGAGFFYGERTHLTVMEYWRWWIVHLWVEGFFEVFATTA
LAFIFSTLGLVSRRMATTASLASASLFMLGGIPGTFHHLYFAGTTTPVMA
VGASFSALEVVPLIVLGHEAWENWRLKTRAPWMENLKWPLMCFVAVAFWN
MLGAGVFGFMINPPVSLYYIQGLNTTPVHAHAALFGVYGFLALGFTLLVL
RYIRPQYALSPGLMKLAFWGLNLGLALMIFTSLLPIGLIQFHASVSEGMW
YARSEAFMQQDILKTLRWGRTFGDVVFLLGALAMVVQVILGLLSGKPAAA

Ligand information

• Ligand ID: LOP
• InChI: InChI=1S/C35H68NO8P/c1-3-5-7-9-11-13-14-15-16-17-18-20-22-24-26-28-35(38)44-33(32-43-45(39,40)42-30-29-36)31-41-34(37)27-25-23-21-19-12-10-8-6-4-2/h15-16,33H,3-14,17-32,36H2,1-2H3,(H,39,40)/b16-15-/t33-/m1/s1
• InChIKey: FUUNMZKPCMPCHT-ILGKRYBBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCCCC\C=C/CCCCCCCC
  CACTVS 3.341: CCCCCCCCCCCC(=O)OC[C@H](CO[P@@](O)(=O)OCCN)OC(=O)CCCCCCC\C=C/CCCCCCCC
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCCN)OC(=O)CCCCCCCC=CCCCCCCCC
  ACDLabs 10.04: O=C(OCC(OC(=O)CCCCCCC\C=C/CCCCCCCC)COP(=O)(OCCN)O)CCCCCCCCCCC
  CACTVS 3.341: CCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OCCN)OC(=O)CCCCCCCC=CCCCCCCCC
• Formula: C35 H68 N O8 P
• Name: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE;
  LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE
• ZINC: ZINC000064437180
• PDB chain: 8bgw Chain A Residue 809

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bgw A 2.2 angstrom cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): V594 A595 F598 F668 W669 A676
• Binding residue (residue number reindexed from 1): V594 A595 F598 F668 W669 A676
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 16:23:23 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 = '8bgw', asym_id = 'B', bs = 'BS03', title = 'A 2.2 angstrom cryoEM structure of a quinol-depe...e shows close similarity to respiratory oxidases.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8bgw', asym_id='B', bs='BS03', title='A 2.2 angstrom cryoEM structure of a quinol-depe...e shows close similarity to respiratory oxidases.')

   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 = '0004129,0009060,0016020,0020037', uniprot = '', pdbid = '8bgw', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004129,0009060,0016020,0020037', uniprot='', pdbid='8bgw', 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>