Structure of PDB 8vdw Chain A

Receptor sequence

>8vdwA (length=326) Species: 29466 (Veillonella parvula)

GTYEKILTIANRIMNGGEITKEEAIELIHTSDDDTMILLAMADKIRQHFN
DNSVDVCAIVNARSGKCPENCKFCAQSAHHNTGVQEYPFMDEESILQAAR
KAKEAGAIRFSIVTSGRNTNNPDEFDQIIHVLGRIKNEIGLEICCSLGLL
TYEQALKLKEVGVTRYHSNIETAPSHFPDICTTHSYEDKMFTIDNAQKAG
IRVCSGGILGLNETLEQRVEMAFELKRLHIDSVPLNILNPVKGTPFESNE
ALRPLDILRTFAVFRFILPNALIRTAGGREVNLRDLQAYALKGGLNGIMV
GGYLTTGGRSPQDDLQMIQDLELTRN

3D structure

• PDB: 8vdw X-Ray Crystal Structure of the biotin synthase from V. parvula
• Chain: A
• Resolution: 1.807 Å

Enzymatic activity

• Enzyme Commision number: 2.8.1.6: biotin synthase.

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	Q46	A	C69 R121 S123 C156 H179 C216 R286 M311	C57 R109 S111 C144 H167 C204 R274 M299
BS02	SAM	A	F85 T126 S158 G160 N181 E183 I220 L250 N251	F73 T114 S146 G148 N169 E171 I208 L238 N239
BS03	SF4	A	C79 E81 C83 F85 C86 S127	C67 E69 C71 F73 C74 S115
BS04	DTB	A	H179 P246 N248 Y315 L316 T317 T318	H167 P234 N236 Y303 L304 T305 T306

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 30 09:39:08 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 = '8vdw', asym_id = 'A', title = 'X-Ray Crystal Structure of the biotin synthase from V. parvula'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='8vdw', asym_id='A', title='X-Ray Crystal Structure of the biotin synthase from V. parvula')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003824,0004076,0009102,0051536', uniprot = '', pdbid = '8vdw', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003824,0004076,0009102,0051536', uniprot='', pdbid='8vdw', 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>