Structure of PDB 5ldb Chain B

Receptor sequence
>5ldbB (length=260) Species: 1297799 (Meiothermus ruber H328) [Search protein sequence]
MKKYRVQPDGRFELKRFDPDDTSAFEGGKQAALEALAVLNRRLEKLQELL
YAEGQHKVLVVLQAMDAGGKDGTIRVVFDGVNPSGVRVASFGVPTEQELA
RDYLWRVHQQVPRKGELVIFNRSHYEDVLVVRVKNLVPQQVWQKRYRHIR
EFERMLADEGTTILKFFLHISKDEQRQRLQERLDNPEKRWKFRMGDLEDR
RLWDRYQEAYEAAIRETSTEYAPWYVIPANKNWYRNWLVSHILVETLEGL
AMQYPQIVIE
3D structure
PDB5ldb Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.
ChainB
Resolution2.3 Å
3D
structure
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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 ADP B G92 V93 P94 R106 R122 E126 D127 V130 G92 V93 P94 R106 R122 E126 D127 V130
BS02 PO4 B A67 G69 K70 D71 A67 G69 K70 D71
BS03 MG B T95 Q97 T95 Q97
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sun Dec 1 12:30:31 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 = '5ldb', asym_id = 'B', title = 'Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.'
 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='5ldb', asym_id='B', title='Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.')
    839 
    840     if go:
=>  841         display_go(go,uniprot,pdbid,asym_id)
    842     return pubmed,uniprot
    843 
global display_go = <function display_go>, go = '0006797,0008976,0016776', uniprot = '', pdbid = '5ldb', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0006797,0008976,0016776', uniprot='', pdbid='5ldb', 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>