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Structure of PDB 8dl2 Chain A Binding Site BS06

Receptor Information >8dl2 Chain A (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] VLHDGFNFDPAIPKADEPLTITFKAPEGSNFYGYADDLYLHSGTGANWTG APTWGDNQNKYRLKKTKDNVWSITLSSSIRHFYSVAPSTPLQTINLIVRD AEGSQQTYDYATLVEDSQNGFIWEEPQKAPLPISGEEKEGIHIHSATSIM LVLYDKDSQGGHKDCVFVTGNFNNWKLDSRYMMKYDETNHCWWITLEELT AGETQFQYFVYSASDGGTYLCDPYCEQALEKGVDTNFPTGAQAPYVSVVS TNPQPYQWSAGEFEMKNKENPVIYELLLRDFTSSGNLAGAMEKLPYLKEL GIDAIELMPVQEFAGNDSWGYNTGLYFALDASYGTQNEYKAFIDACHQNG IAVIFDVVYNHTNNDNPFARMYWDTFNNRPSTKNPWLNAVTPHQKYVFSP DDFNHTSEQTKAFVKRNLKYLLDTYHIDGFRFDFTKGFTQKQTTGDDDLA ATDPARVSVLKEYYEAVKAVKEDAMVTMEHFCANEETTLATEGIHFWRNM NHSYCQSAMGWKDNSDFSGLYDTTRPNQFVGYMESHDEERCAYKQIEYGN GALKTNLSERLKQLSSNAAFFFTVPGPKMLWQFGEMGYDISIDENGRTGK KPVLWEYQTERKSLVDIYTKLITLRTTHSDLFNASSQFTWKVSYNDWDNG RTLTLKAVNGKQLHVYANFTNASIDYTIPEGTWYLYLEGNPVEGEKKISV 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 J 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) W363 Y365 F442 D477 F478 E523 H580 D581 Binding residue (residue number reindexed from 1) W319 Y321 F398 D433 F434 E479 H536 D537 Annotation score 1

Gene Ontology --> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed May 21 20:49:07 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 = 'A', bs = 'BS06', 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='A', bs='BS06', 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 = 'A'

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

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>