Structure of PDB 8bgw Chain B Binding Site BS05

Receptor Information
>8bgw Chain B (length=750) Species: 85698 (Achromobacter xylosoxidans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGPYRRLWFTLIAVLAVTFALLGFYGGEVYRQAPPIPEEVASADGTRLFG
RDDILDGQTAWQSIGGMQLGSIWGHGAYQAPDWTADWLHRELMAWLDLAA
RDAHGRDYGQLDAPAQAALREQLKAEYRANRADAAGGKLTLSPRRAQAVA
QTEAYYDQLFSDAPALHRSRENYAMKENTLPDANRRRQMTHFFFWTAWAA
ATEREGTSVTYTNNWPHEPLIGNHPSSENVMWSIISVVVLLAGIGLLIWA
WAFLRGKEEDEPPAPARDPLTTFALTPSQRALGKYLFLVVALFGFQVLLG
GFTAHYTVEGQKFYGIDLSQWFPYSLVRTWHIQSALFWIATGFLAAGLFL
APLINGGRDPKYQKAGVDILFWALVLVVVGSFAGNYLAIAQIMPPDLNFW
LGHQGYEYVDLGRLWQIGKFAGICFWLVLMLRGIVPALRTPGGDKNLLAL
LTASVGAIGLFYGAGFFYGERTHLTVMEYWRWWIVHLWVEGFFEVFATTA
LAFIFSTLGLVSRRMATTASLASASLFMLGGIPGTFHHLYFAGTTTPVMA
VGASFSALEVVPLIVLGHEAWENWRLKTRAPWMENLKWPLMCFVAVAFWN
MLGAGVFGFMINPPVSLYYIQGLNTTPVHAHAALFGVYGFLALGFTLLVL
RYIRPQYALSPGLMKLAFWGLNLGLALMIFTSLLPIGLIQFHASVSEGMW
YARSEAFMQQDILKTLRWGRTFGDVVFLLGALAMVVQVILGLLSGKPAAA
Ligand information
Ligand ID10M
InChIInChI=1S/C22H42O10S/c1-2-3-4-5-6-7-8-9-10-33-22-19(29)17(27)20(14(12-24)31-22)32-21-18(28)16(26)15(25)13(11-23)30-21/h13-29H,2-12H2,1H3/t13-,14-,15-,16+,17-,18-,19-,20-,21-,22+/m1/s1
InChIKeyYZNNXXWNKQOETJ-HYLFJBCQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCSC1C(C(C(C(O1)CO)OC2C(C(C(C(O2)CO)O)O)O)O)O
ACDLabs 10.04S(CCCCCCCCCC)C2OC(C(OC1OC(CO)C(O)C(O)C1O)C(O)C2O)CO
OpenEye OEToolkits 1.5.0CCCCCCCCCCS[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O
CACTVS 3.341CCCCCCCCCCS[CH]1O[CH](CO)[CH](O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O
CACTVS 3.341CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O
FormulaC22 H42 O10 S
Namedecyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside;
(2R,3R,4S,5S,6R)-2-((2R,3S,4R,5R,6S)-6-Decylsulfanyl-4,5-dihydroxy-2-hydroxymethyl-tetrahydro-pyran-3-yloxy)-6-hydroxymethyl-tetrahydro-pyran-3,4,5-triol, n-Decyl-beta-D-thiomaltoside
ChEMBL
DrugBank
ZINCZINC000014114498
PDB chain8bgw Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8bgw A 2.2 angstrom cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H224 P225 S227 V230 S233 I234 V237 P613 V615
Binding residue
(residue number reindexed from 1)		H224 P225 S227 V230 S233 I234 V237 P613 V615
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 16:23:43 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 = 'BS05', 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='BS05', 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>