Structure of PDB 6rtg Chain A Binding Site BS01

Receptor Information

>6rtg Chain A (length=503) Species: 349967 (Yersinia mollaretii ATCC 43969)

NNFITHNLHTVWIGGPLPDITKSYLKVWRDINPDYTHITWIDTDNKFVAL
YNNAVKELREYTLKQYLVGDSNATANDYYDQAVQIERGVRENVYLPHGND
IERIKTIKKIAGSLGDNKVQEYRTKIETIESSFVEMIDGGHYQHVSALFE
QFSEMDNLRATALKQIYEREINDRGNLAAASDILRLVALQTQGGVYIDTD
LLPHIDWDLIESTKLFLDNNSVERVYSKEIYLEIEKYKQLTGSKTNKIRS
GLTKSQINEIQRLTEENNLFKHLNELEKNCFYSDNSVRGWTNAMLACNEN
NGFMNALMDRIILNYTILDEFIISNIVTDGEMLNFTEKMSAQFGLNAEHE
GSFIPSLANYYKDSIVPNSPQATATLFMTGPTVLDTVIRVEEAVRRGIVK
KEAIASLYTVEETFSSWSISQFYDKAAFYLDKVKFDISLNSAEEGILRDS
CFDVIQQSKEQATHLPDIAIKFLESLNNFTWKQLELLIKASEFSDQYKTL
ATL

Ligand information

• Ligand ID: UDP
• InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: XCCTYIAWTASOJW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.370: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
• Formula: C9 H14 N2 O12 P2
• Name: URIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL130266
• DrugBank: DB03435
• ZINC: ZINC000004490939
• PDB chain: 6rtg Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rtg Inverse control of Rab proteins byYersiniaADP-ribosyltransferase and glycosyltransferase related to clostridial glucosylating toxins.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): V22 W23 I24 L190 S194 D211 T212 D213 S430 S431 W432
• Binding residue (residue number reindexed from 1): V11 W12 I13 L177 S181 D198 T199 D200 S415 S416 W417
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Feb 22 18:04:59 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 = '6rtg', asym_id = 'A', bs = 'BS01', title = 'Inverse control of Rab proteins byYersiniaADP-ri...ase related to clostridial glucosylating toxins. '

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6rtg', asym_id='A', bs='BS01', title='Inverse control of Rab proteins byYersiniaADP-ri...ase related to clostridial glucosylating toxins. ')

   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 = '6rtg', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016757', uniprot='', pdbid='6rtg', 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>