Structure of PDB 8bgw Chain B Binding Site BS01

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 A Residue 805 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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 V615 S616 Y619 V695
Binding residue
(residue number reindexed from 1)		H224 V615 S616 Y619 V695
Annotation score1
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 16:53:14 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 = 'BS01', 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='BS01', 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>