Structure of PDB 6vzb Chain A

Receptor sequence

>6vzbA (length=393) Species: 1463854 (Streptomyces sp. NRRL F-5053)

TLTYPFHDWSQELSPRYAQLRASDAPVCPVVSEGTGDPLWLVTRYATAVK
LLEDSRFSSEAAQASGAPRQEPVELRAPGTRGDAIAMLREAGLRSVLADG
LGPRAVRRHQGWINDLAETLMSELASREGTFDLAADFVEPLSSALVSRTL
LGELSADERDLLAHCADTGLRFCGVTHEEQVHAFTQMHEFFLEHARRLAG
TPGEHLLKLIAEAPVPLSDEALAEAGSLLVVAGFPTSSGFLCGALLTLLR
HPDAVQELHAHPERVPSAVEELLRYTPLATGSAKRMATEDLEIDGVRIKA
GEVVMVSLEAVNHDPDAFEDPDVFRPGREGPMHFGFGRGRHFCPGNRLAR
CVIEATVRAVARRPGLRLAVAPEEISWHEGLFFRRPRAIPATW

3D structure

• PDB: 6vzb Molecular basis of regio- and stereo-specificity in biosynthesis of bacterial heterodimeric diketopiperazines.
• Chain: A
• Resolution: 1.68 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	QRP	A	Q72 T241 A284 G286 A288 K289 L313 F387 F388	Q70 T236 A279 G281 A283 K284 L308 F382 F383	MOAD: Kd=4.81uM
BS02	QRP	A	Q65 K289 F388	Q63 K284 F383	MOAD: Kd=4.81uM
BS03	HEM	A	L152 A237 G238 S242 R290 G340 F341 H346 C348 P349 G350 A354	L150 A232 G233 S237 R285 G335 F336 H341 C343 P344 G345 A349

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 22 11:17:55 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 = '6vzb', asym_id = 'A', title = 'Molecular basis of regio- and stereo-specificity...sis of bacterial heterodimeric diketopiperazines.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6vzb', asym_id='A', title='Molecular basis of regio- and stereo-specificity...sis of bacterial heterodimeric diketopiperazines.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0004497,0005506,0016705,0020037', uniprot = '', pdbid = '6vzb', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004497,0005506,0016705,0020037', uniprot='', pdbid='6vzb', 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>