Structure of PDB 8dl2 Chain A Binding Site BS02

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 IDAC1
InChIInChI=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
InChIKeyRBZIIHWPZWOIDU-ZCGMLSCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)O)O)O)NC2C=C(C(C(C2O)O)O)CO
CACTVS 3.341C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1N[CH]2C=C(CO)[CH](O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C[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 10.04OC2C(NC1C=C(CO)C(O)C(O)C1O)C(OC(O)C2O)C
CACTVS 3.341C[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
FormulaC13 H23 N O8
Name4,6-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
DrugBankDB02218
ZINCZINC000058638973
PDB chain8dl2 Chain H Residue 3 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8dl2 BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		H85 W92 D153
Binding residue
(residue number reindexed from 1)		H41 W48 D109
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon Nov 25 12:22:12 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 = '8dl2', asym_id = 'A', bs = 'BS02', 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='BS02', 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 = '8dl2', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005975', uniprot='', pdbid='8dl2', 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>