Structure of PDB 1v5f Chain A Binding Site BS03

Receptor Information

>1v5f Chain A (length=589) Species: 1377 (Aerococcus viridans)

NKINIGLAVMKILESWGADTIYGIPSGTLSSLMDAMGEEENNVKFLQVKH
EEVGAMAAVMQSKFGGNLGVTVGSGGPGASHLINGLYDAAMDNIPVVAIL
GSRPQRELNMDAFQELNQNPMYDHIAVYNRRVAYAEQLPKLVDEAARMAI
AKRGVAVLEVPGDFAKVEIDNDQWYSSANSLRKYAPIAPAAQDIDAAVEL
LNNSKRPVIYAGIGTMGHGPAVQELARKIKAPVITTGKNFETFEWDFEAL
TGSTYRVGWKPANETILEADTVLFAGSNFPFSEVEGTFRNVDNFIQIDID
PAMLGKRHHADVAILGDAALAIDEILNKVDAVEESAWWTANLKNIANWRE
YINMLETKEEGDLQFYQVYNAINNHADEDAIYSIDVGNSTQTSIRHLHMT
PKNMWRTSPLFATMGIAIPGGLGAKNTYPDRQVWNIIGDGAFSMTYPDVV
TNVRYNMPVINVVFSNTEYAFIKNKYEDTNKNLFGVDFTDVDYAKIAEAQ
GAKGFTVSRIEDMDRVMAEAVAANKAGHTVVIDCKITQDRPIPVETLKLD
SKLYSEDEIKAYKERYEAANLVPFREYLEAEGLESKYIK

Ligand information

• Ligand ID: TPP
• InChI: InChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
• InChIKey: AYEKOFBPNLCAJY-UHFFFAOYSA-O
• SMILES:
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
• Formula: C12 H19 N4 O7 P2 S
• Name: THIAMINE DIPHOSPHATE
• ChEMBL: CHEMBL1236376
• ZINC: ZINC000008215517
• PDB chain: 1v5f Chain A Residue 1602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1v5f The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): N391 S392 M417 G441 G443 N469 Y472 A473 F474 I475
• Binding residue (residue number reindexed from 1): N388 S389 M414 G438 G440 N466 Y469 A470 F471 I472
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 29 02:41:03 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 = '1v5f', asym_id = 'A', bs = 'BS03', title = 'The structures of pyruvate oxidase from Aerococc...ibility of the active-site tunnel for catalysis. '

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='1v5f', asym_id='A', bs='BS03', title='The structures of pyruvate oxidase from Aerococc...ibility of the active-site tunnel for catalysis. ')

   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 = '0000287,0003824,0030976,0047112', uniprot = '', pdbid = '1v5f', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000287,0003824,0030976,0047112', uniprot='', pdbid='1v5f', 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>