Structure of PDB 8p20 Chain CCC Binding Site BS01

Receptor Information
>8p20 Chain CCC (length=492) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKQTYMIVNELDVNKGGMTTAMLTRSKFFLDNEISGDIITFDFKANYKDI
LKELVQSKKMDKRTQMHNPFIYFKNISNLQHKKYNYTMTRNLSNLLKDSV
EIKENSRISRFFNIMSREYLAYKRETEQETIFDLFKNNLRYKRIYFYKGK
IVKTEVFNSDNNLIAEQFYDDNGYLYLYRQINPEKKSIGKTYLVCKEKQF
KNNVEFCSYFLDKLIPDINDNIIICDGPGSFPKILKTNHKNVKKFAVIHV
NHYKNFDDTGAVKKQEDYILRNANKINGVVMLTEAQKKDIIEKYKITNAY
VISNFINITDDYRDKNDNKVVGHISRLVPQKGLPYLIDVAKKVVEQDNSV
EFHLYGTGEEKSKIENLIQESNLTNNVKLLGYTTNAIEKIKDFRCVISTS
QFEGQGLSLIEAMLLKKPVVAFDVKYGPSDFVKDGKNGYLIENKDIKKMA
NKILKLLHDKELSKSLGKHGRDTIIDMYQPEKLMVKWKQLFN
Ligand information
Ligand IDBJT
InChIInChI=1S/C26H56O34P4/c27-1-10(29)19(36)12(31)4-53-62(46,47)54-5-14(33)21(38)15(34)6-55-63(48,49)57-8-16(35)22(39)18(60-26-25(42)24(41)23(40)17(2-28)59-26)9-58-64(50,51)56-7-13(32)20(37)11(30)3-52-61(43,44)45/h10-42H,1-9H2,(H,46,47)(H,48,49)(H,50,51)(H2,43,44,45)/t10-,11+,12+,13-,14-,15+,16-,17-,18+,19-,20+,21-,22-,23-,24+,25-,26-/m0/s1
InChIKeyDYIPZANUDJDCKR-AXBQPTFUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C(C1C(C(C(C(O1)OC(COP(=O)(O)OCC(C(C(COP(=O)(O)O)O)O)O)C(C(COP(=O)(O)OCC(C(C(COP(=O)(O)OCC(C(C(CO)O)O)O)O)O)O)O)O)O)O)O)O
CACTVS 3.385OC[CH](O)[CH](O)[CH](O)CO[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO[P](O)(=O)OC[CH](O)[CH](O)[CH](CO[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)O[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
CACTVS 3.385OC[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)OC[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)OC[C@H](O)[C@H](O)[C@@H](CO[P](O)(=O)OC[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)O[C@@H]1O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.7C([C@H]1[C@@H]([C@H]([C@@H]([C@@H](O1)O[C@H](COP(=O)(O)OC[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)[C@H]([C@H](COP(=O)(O)OC[C@H]([C@H]([C@H](COP(=O)(O)OC[C@H]([C@H]([C@H](CO)O)O)O)O)O)O)O)O)O)O)O)O
FormulaC26 H56 O34 P4
Name[(2~{R},3~{S},4~{S})-2-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentoxy]phosphoryl]oxy-pentoxy]phosphoryl]oxy-pentyl] [(2~{S},3~{R},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain8p20 Chain CCC Residue 501 [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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PDB8p20 Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition.
Resolution2.848 Å
Binding residue
(original residue number in PDB)		N9 G16 M18 T19 G227 P228 G229 S230 K233 V250 N255 K263 Q265 R326 F402
Binding residue
(residue number reindexed from 1)		N9 G16 M18 T19 G227 P228 G229 S230 K233 V250 N255 K263 Q265 R326 F402
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Wed Feb 19 04:52:50 2025

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 = '8p20', asym_id = 'CCC', bs = 'BS01', title = 'Invasive Staphylococcus epidermidis uses a uniqu... glycosyltransferase to evade immune recognition.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8p20', asym_id='CCC', bs='BS01', title='Invasive Staphylococcus epidermidis uses a uniqu... glycosyltransferase to evade immune recognition.')
   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 = '0016757', uniprot = '', pdbid = '8p20', asym_id = 'CCC'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016757', uniprot='', pdbid='8p20', asym_id='CCC')
    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>