Structure of PDB 4x47 Chain A Binding Site BS01

Receptor Information

>4x47 Chain A (length=489) Species: 411470 (Mediterraneibacter gnavus ATCC 29149)

GAMADIGSNIFYAGDATKSNYFRIPSLLALDSGTVIAAADARYGGTHDAK
SKINTAFAKSTDGGKTWGQPTLPLKFDDYVAKNIDWPRDSVGKNVQIQGS
ASYIDPVLLEDKETHRVFLFADMMPAGIGSSNASVGSGFKEVDGKKYLKL
HWKDDAAGTYDYSVRENGTIYNDTTNSATEYSVDGEYNLYKNGNAMLCKQ
YDYNFEGTKLLETQTDTDVNMNVFYKDADFKVFPTTYLAMKYSDDEGETW
SDLQIVSTFKPEESKFLVLGPGVGKQIANGEHAGRLIVPLYSKSSAELGF
MYSDDHGNNWTYVEADQNTGGATAEAQIVEMPDGSLKTYLRTGSGYIAQV
MSTDGGETWSERVPLTEIATTGYGTQLSVINYSQPVDGKPAILLSAPNAT
NGRKNGKIWIGLISETGNSGKDKYSVDWKYCYSVDTPQMGYSYSCLTELP
DGEIGLLYEKYDSWSRNELHLKNILKYERFNIDELKVQP

Ligand information

• Ligand ID: DAN
• InChI: InChI=1S/C11H17NO8/c1-4(14)12-8-5(15)2-7(11(18)19)20-10(8)9(17)6(16)3-13/h2,5-6,8-10,13,15-17H,3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,8+,9+,10+/m0/s1
• InChIKey: JINJZWSZQKHCIP-UFGQHTETSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C=1OC(C(O)C(O)CO)C(NC(=O)C)C(O)C=1
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C=C(OC1C(C(CO)O)O)C(=O)O)O
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H]1[C@H](C=C(O[C@H]1[C@@H]([C@@H](CO)O)O)C(=O)O)O
  CACTVS 3.341: CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C=C(O[CH]1[CH](O)[CH](O)CO)C(O)=O
• Formula: C11 H17 N O8
• Name: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID;
  Neu5Ac2en
• ChEMBL: CHEMBL96712
• DrugBank: DB03991
• ZINC: ZINC000004096465
• PDB chain: 4x47 Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4x47 Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R257 D282 D339 T557 R575 R637 Y677 W698
• Binding residue (residue number reindexed from 1): R23 D48 D105 T323 R341 R403 Y443 W464
• Annotation score: 1
• Binding affinity: MOAD: ic50=1.41mM
  PDBbind-CN: -logKd/Ki=2.85,IC50=1.41mM

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Nov 24 17:45:42 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 = '4x47', asym_id = 'A', bs = 'BS01', title = 'Discovery of intramolecular trans-sialidases in ... suggests novel mechanisms of mucosal adaptation.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4x47', asym_id='A', bs='BS01', title='Discovery of intramolecular trans-sialidases in ... suggests novel mechanisms of mucosal adaptation.')

   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 = '0004308', uniprot = '', pdbid = '4x47', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004308', uniprot='', pdbid='4x47', 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>