Structure of PDB 4jdz Chain B

Receptor sequence
>4jdzB (length=445) Species: 548473 (Staphylococcus aureus subsp. aureus TCH60) [Search protein sequence]
SKNVNDLITSNTTLTVVDAIKNNKIVPAQDYLALKSQIKVDDKVKSGDYF
TIKYSDTVQVYGLNPEDIKNIGDIKDPNNGETIATAKHDTANNLITYTFT
DYVDRFNSVQMGINYSIYMDADTIPVSKNDVEFNVTIGNDTTKTTANIQY
PDYVSRDNNSIGSAFTETVSHAGNAEDPGYYKQTVYVNPSEKSLTNAKLK
VEAYHKDYPDNVGQINKDVTKIKIYQAPKDYVLNKGYDVNTNQLIDVTEQ
FKDKITYGANDSVNVDFGSINNSYVVMVDTKFEYTTSASPTLVQMATLTS
DGNRSVSTGNALGFTNNQSGGAAQEVYKIGNYVWEDTNKNGVQDLGEVGV
KGVTVVAYDNAAAAEVGRTITDDKGGYLIPNLPNGDYRVEFSNLPQGYEV
TPSKQGNNEELDSNGVSSVITVNGKDNLSADLGIYKPKYNLGDYA
3D structure
PDB4jdz Structures of SdrD from Staphylococcus aureus reveal the molecular mechanism of how the cell surface receptors recognize their ligands
ChainB
Resolution2.1 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 CA B N565 L663 D666 N331 L428 D431
BS02 CA B E644 D647 N649 S664 E409 D412 N414 S429
BS03 CA B D570 N572 N574 V576 D578 E581 D336 N338 N340 V342 D344 E347
BS04 CA B D252 N256 K258 D264 D18 N22 K24 D30
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Tue Mar 4 16:22:53 2025

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 = '4jdz', asym_id = 'B', title = 'Structures of SdrD from Staphylococcus aureus re...e cell surface receptors recognize their ligands '
 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4jdz', asym_id='B', title='Structures of SdrD from Staphylococcus aureus re...e cell surface receptors recognize their ligands ')
    839 
    840     if go:
=>  841         display_go(go,uniprot,pdbid,asym_id)
    842     return pubmed,uniprot
    843 
global display_go = <function display_go>, go = '0005618,0007155', uniprot = '', pdbid = '4jdz', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005618,0007155', uniprot='', pdbid='4jdz', asym_id='B')
    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>