Structure of PDB 6d9b Chain A Binding Site BS02

Receptor Information

>6d9b Chain A (length=386) Species: 1717 (Corynebacterium diphtheriae)

SDFDLIVVGSGLFGLTVAERAASQLGKKVLIVEKRSHLGGNAYSEAEPET
GIEIHKYGAHLFHTSNKRVWDYVNQFTAFTGYQHRVFAMHNGTAYQFPMG
LGLINQFFGRYYTPDEARELIKEQSAEIDSKDATNLEEKAISLIGRPLYE
AFIRDYTAKQWQTDPKELPAGNITRLPVRYNFDNRYFNDTYEGLPVDGYA
QWLSNMADHENIEVRLDTDWFEVREDLRAQNPEAPVVYTGPLDRYFDYSE
GHLGWRTLDFETEVLNTGDFQGTPVMNYNDAEFPYTRIHEFRHFHPERED
RHPKDKTVIMKEYSRFAEEGDEPYYPINTPSDREMLFKYRELADAETESG
KVYFGGRLGTYQYLDMHMAIASALSMFDNKLVDALK

Ligand information

• Ligand ID: UPG
• InChI: InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
• InChIKey: HSCJRCZFDFQWRP-JZMIEXBBSA-N
• SMILES:
  CACTVS 3.370: OC[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 12.01: O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O
  CACTVS 3.370: OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
• Formula: C15 H24 N2 O17 P2
• Name: URIDINE-5'-DIPHOSPHATE-GLUCOSE;
  URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
• ChEMBL: CHEMBL375951
• DrugBank: DB01861
• ZINC: ZINC000008215472
• PDB chain: 6d9b Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d9b Substrate recognition by FAD in UDP-galactopyranose mutase
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): F98 F153 I154 Y157 T158 Q161 Y187 N278 R288 D366
• Binding residue (residue number reindexed from 1): F97 F152 I153 Y156 T157 Q160 Y186 N277 R287 D365
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Nov 25 16:17:42 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 = '6d9b', asym_id = 'A', bs = 'BS02', title = 'Substrate recognition by FAD in UDP-galactopyranose mutase'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6d9b', asym_id='A', bs='BS02', title='Substrate recognition by FAD in UDP-galactopyranose mutase')

   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 = '0008767', uniprot = '', pdbid = '6d9b', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008767', uniprot='', pdbid='6d9b', asym_id='A')

    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>