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Structure of PDB 8dl2 Chain D Binding Site BS04

Receptor Information >8dl2 Chain D (length=712) Species: 411476 (Bacteroides ovatus ATCC 8483) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] QVLHDGFNFDPAIPKADEPLTITFKAPEGSNFYGYADDLYLHSGTGANWT GAPTWGDNQNKYRLKKTKDNVWSITLSSSIRHFYSVAPSTPLQTINLIVR DAEGSQQTYDYATLVEDSQNGFIWEEPQKAPLPISGEEKEGIHIHSATSI MLVLYDKDSQGGHKDCVFVTGNFNNWKLDSRYMMKYDETNHCWWITLEEL TAGETQFQYFVYSASDGGTYLCDPYCEQALEKGVDTNFPTGAQAPYVSVV STNPQPYQWSAGEFEMKNKENPVIYELLLRDFTSSGNLAGAMEKLPYLKE LGIDAIELMPVQEFAGNDSWGYNTGLYFALDASYGTQNEYKAFIDACHQN GIAVIFDVVYNHTNNDNPFARMYWDTFNNRPSTKNPWLNAVTPHQKYVFS PDDFNHTSEQTKAFVKRNLKYLLDTYHIDGFRFDFTKGFTQKQTTGDDDL AATDPARVSVLKEYYEAVKAVKEDAMVTMEHFCANEETTLATEGIHFWRN MNHSYCQSAMGWKDNSDFSGLYDTTRPNQFVGYMESHDEERCAYKQIEYG NGALKTNLSERLKQLSSNAAFFFTVPGPKMLWQFGEMGYDISIDENGRTG KKPVLWEYQTERKSLVDIYTKLITLRTTHSDLFNASSQFTWKVSYNDWDN GRTLTLKAVNGKQLHVYANFTNASIDYTIPEGTWYLYLENGNPVEKKISV PAHEFRLYTNFA

Ligand information Ligand ID AC1 InChI InChI=1S/C13H23NO8/c1-4-7(10(18)12(20)13(21)22-4)14-6-2-5(3-15)8(16)11(19)9(6)17/h2,4,6-21H,3H2,1H3/t4-,6+,7-,8-,9+,10+,11+,12-,13+/m1/s1 InChIKey RBZIIHWPZWOIDU-ZCGMLSCUSA-N SMILES Software SMILES OpenEye OEToolkits 1.5.0 CC1C(C(C(C(O1)O)O)O)NC2C=C(C(C(C2O)O)O)CO CACTVS 3.341 C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1N[CH]2C=C(CO)[CH](O)[CH](O)[CH]2O OpenEye OEToolkits 1.5.0 C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO ACDLabs 10.04 OC2C(NC1C=C(CO)C(O)C(O)C1O)C(OC(O)C2O)C CACTVS 3.341 C[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1N[C@H]2C=C(CO)[C@@H](O)[C@H](O)[C@H]2O Formula C13 H23 N O8 Name 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose; 6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL; 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucose; 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-D-glucose; 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-glucose ChEMBL DrugBank DB02218 ZINC ZINC000058638973 PDB chain 8dl2 Chain Q Residue 3 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 8dl2 BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut. Resolution 1.99 Å Binding residue (original residue number in PDB) H85 N91 W92 D153 Binding residue (residue number reindexed from 1) H42 N48 W49 D110 Annotation score 1

Gene Ontology --> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed May 21 02:12:43 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>()

1701     title=pdb2title(pdbid)

1702     if bs.startswith("BS"):

=> 1703         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

1704     else:

1705         if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '8dl2', asym_id = 'D', bs = 'BS04', 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='8dl2', asym_id='D', bs='BS04', title='BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.')

1326         display_ec(ec,csaOrig,csaRenu)

1327     if go:

=> 1328         display_go(go,uniprot,pdbid,asym_id)

1329     return pubmed,uniprot

1330

global display_go = <function display_go>, go = '0005975', uniprot = '', pdbid = '8dl2', asym_id = 'D'

/var/www/html/BioLiP/pdb.cgi in display_go(go='0005975', uniprot='', pdbid='8dl2', asym_id='D')

484         '''.replace("$namespace_link",namespace_link

485           ).replace("$namespace",namespace

=>  486           ).replace("$uniprot",u

487         ))

488         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>