Structure of PDB 8dl1 Chain A Binding Site BS09

Receptor Information

>8dl1 Chain A (length=713) Species: 411476 (Bacteroides ovatus ATCC 8483)

VLHDGFNFDPAIPKADEPLTITFKAPEGSNFYGYADDLYLHSGTGANWTG
APTWGDNQNKYRLKKTKDNVWSITLSSSIRHFYSVAPSTPLQTINLIVRD
AEGSQQTYDYATLVEDSQNGFIWEEPQKAPLPISGEEKEGIHIHSATSIM
LVLYDKDSQGGHKDCVFVTGNFNNWKLDSRYMMKYDETNHCWWITLEELT
AGETQFQYFVYSASDGGTYLCDPYCEQALEKGVDTNFPTGAQAPYVSVVS
TNPQPYQWSAGEFEMKNKENPVIYELLLRDFTSSGNLAGAMEKLPYLKEL
GIDAIELMPVQEFAGNDSWGYNTGLYFALDASYGTQNEYKAFIDACHQNG
IAVIFDVVYNHTNNDNPFARMYWDTFNNRPSTKNPWLNAVTPHQKYVFSP
DDFNHTSEQTKAFVKRNLKYLLDTYHIDGFRFDFTKGFTQKQTTGDDDLA
ATDPARVSVLKEYYEAVKAVKEDAMVTMQHFCANEETTLATEGIHFWRNM
NHSYCQSAMGWKDNSDFSGLYDTTRPNQFVGYMESHDEERCAYKQIEYGN
GALKTNLSERLKQLSSNAAFFFTVPGPKMLWQFGEMGYDISIDENGRTGK
KPVLWEYQTERKSLVDIYTKLITLRTTHSDLFNASSQFTWKVSYNDWDNG
RTLTLKAVNGKQLHVYANFTNASIDYTIPEGTWYLYLEGNPVEGEKKISV
PAHEFRLYTNFAE

Ligand information

• Ligand ID: GLC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-DVKNGEFBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-glucopyranose;
  alpha-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL423707
• ZINC: ZINC000003861213
• PDB chain: 8dl1 Chain O Residue 4

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dl1 BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
• Resolution: 2.09 Å
• Binding residue (original residue number in PDB): W363 Y365 H405 F442 D477 Q523 H580 D581
• Binding residue (residue number reindexed from 1): W319 Y321 H361 F398 D433 Q479 H536 D537
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 22 17:29:15 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 = '8dl1', asym_id = 'A', bs = 'BS09', title = 'BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8dl1', asym_id='A', bs='BS09', title='BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.')

   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 = '0005975', uniprot = '', pdbid = '8dl1', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005975', uniprot='', pdbid='8dl1', 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>