Structure of PDB 8jjq Chain C Binding Site BS01

Receptor Information

>8jjq Chain C (length=321) Species: 34073 (Variovorax paradoxus)

SNPSLVIVSPALPGANNGNWRTAQRWKALLSPVCSARVVQQWPDADASAD
TVMLALHARRSAESIAHWAHAHPGRGLGVVLTGTDLYQDIGSDPQAQRSL
QLAQRLVVLQALGAEALPPECRAKARVVYQSTSARAELPKSARQLRAVMV
GHLRQVKSPQTLFDAARLLCGREDIRIDHIGDAGDAGLGELARALASDCP
GYRWLGALPHAQTRQRIQRAHVLVHTSALEGGAHVIMEAVRSGTPVLASR
VPGNVGMLGNDYAGYFPHGDAAALAALLEACRAGQGAGLLDSLRTQCALR
APLFDPRAEQAALFQLLNELQ

Ligand information

• Ligand ID: UD2
• InChI: InChI=1S/C17H27N3O17P2/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)36-39(31,32)37-38(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11+,12-,13-,14-,15-,16-/m1/s1
• InChIKey: LFTYTUAZOPRMMI-NESSUJCYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
  ACDLabs 10.04: O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
• Formula: C17 H27 N3 O17 P2
• Name: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE;
  (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
• DrugBank: DB02196
• ZINC: ZINC000008551132
• PDB chain: 8jjq Chain C Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jjq Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms resolution
• Resolution: 1.64 Å
• Binding residue (original residue number in PDB): N17 G19 N20 R22 T23 T83 L110 H153 R155 K158 I181 L209 H211 T214 E231 G232 G233 A234 H235 V236 E239
• Binding residue (residue number reindexed from 1): N16 G18 N19 R21 T22 T82 L109 H152 R154 K157 I180 L208 H210 T213 E230 G231 G232 A233 H234 V235 E238
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Dec 1 00:46:20 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 = '8jjq', asym_id = 'C', bs = 'BS01', title = 'Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms resolution'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8jjq', asym_id='C', bs='BS01', title='Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms resolution')

   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 = '8jjq', asym_id = 'C'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016757', uniprot='', pdbid='8jjq', asym_id='C')

    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>