Structure of PDB 8dl1 Chain D

Receptor sequence

>8dl1D (length=706) Species: 411476 (Bacteroides ovatus ATCC 8483)

VLHDGFNFDPAIPKADEPLTITFKAPEGSNFYGYADDLYLHSGTGANWTG
APTWGDNQNKYRLKKTKDNVWSITLSSSIRHFYSVAPSTPLQTINLIVRD
AEGSQQTYDYATLVEDSQNGFIWEEPQKAPLPISEEKEGIHIHSATSIML
VLYDKDSQGGHKDCVFVTGNFNNWKLDSRYMMKYDETNHCWWITLEELTA
GETQFQYFVYSASDGGTYLCDPYCEQALEKGVDTNFPTGAQAPYVSVVST
NPQPYQWSFEMKNKENPVIYELLLRDFTSSGNLAGAMEKLPYLKELGIDA
IELMPVQEFAGNDSWGYNTGLYFALDASYGTQNEYKAFIDACHQNGIAVI
FDVVYNHTNNDNPFARMYWDTFNNRPSTKNPWLNAVTPHQKYVFSPDDFN
HTSEQTKAFVKRNLKYLLDTYHIDGFRFDFTKGFTQKQTTGDDDLAATDP
ARVSVLKEYYEAVKAVKEDAMVTMQHFCANEETTLATEGIHFWRNMNHSY
CQSAMGWKDNSDFSGLYDTTRPNQFVGYMESHDEERCAYKQIEYGNGALK
TNLSERLKQLSSNAAFFFTVPGPKMLWQFGEMGYDISIDENGRTGKKPVL
WEYQTERKSLVDIYTKLITLRTTHSDLFNASSQFTWKVSYNDWDNGRTLT
LKAVNGKQLHVYANFTNASIDYTIPEGTWYLYLEGNPVEKKISVPAHEFR
LYTNFA

3D structure

• PDB: 8dl1 BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
• Chain: D
• Resolution: 2.09 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	GLC	D	W98 Q150	W54 Q106
BS02	GLC	D	H85 W92 D153	H41 W48 D109
BS03	GLC	D	N91 W92	N47 W48
BS04	GLC	D	K588 Y592	K540 Y544
BS05	GLC	D	Q550 W555 Y592	Q502 W507 Y544
BS06	GLC	D	W555 D557	W507 D509
BS07	GLC	D	F478 Q523	F430 Q475
BS08	GLC	D	W363 F442 D477 Q523 H580 D581	W315 F394 D429 Q475 H532 D533
BS09	GLC	D	W363 Y365 R641	W315 Y317 R593
BS10	GLC	D	S362 W363 Y365 N366	S314 W315 Y317 N318
BS11	CA	D	E274 E356 F357 G359 D374	E229 E308 F309 G311 D326
BS12	MN	D	N404 H437 D446 G481	N356 H389 D398 G433

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Tue Nov 26 07:06:44 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>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '8dl1', asym_id = 'D', title = 'BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.'

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

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0005975', uniprot = '', pdbid = '8dl1', asym_id = 'D'

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

    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>